A Comprehensive Resource for Candida glabrata Genome

Acid-fast - A property of cell walls that during a staining reaction retain basic dyes when decolorized with mineral acids.

Accession number - This refers to the unique GenBank identifier a sequence has been assigned. This number can be used to search Genbank records for a specific sequence

Acropetal - Having the youngest conidia at the apex of a chain.

Actinomycete - A Gram-positive bacterium that grows vegetatively in a branched filamentous form.

Aerial hyphae - Hyphae that grow above the agar surface.

Aerobic - Having the ability to grow in the presence of oxygen.

Agar - A polysaccharide produced by a red algae. It is used to gel culture media for growing microorganisms.

Allantoid - Sausage shaped.

Algorithm - A series of steps defining a procedure or formula for solving a problem, that can be coded into a programming language and executed. Bioinformatics algorithms typically are used to process, store, analyze, visualize and make predictions from biological data.

Alignment - The result of a comparison of two or more gene or protein sequences in order to determine their degree of base or amino acid similarity. Sequence alignments are used to determine the similarity, homology, function or other degree of relatedness between two or more genes or gene products.

Allele - A given form of a gene that occupies a specific position or locus on a chromosome. Variant forms of genes occurring at the same locus are said to be alleles of one another.

Anaerobic - Lacking the ability to grow in the presence of oxygen.

Analogy - Reasoning by which the function of a novel gene or protein sequence may be deduced from comparisons with other gene or protein sequences of known function. Identifying analogous or homologous genes via similarity searching and alignment is one of the chief uses of Bioinformatics.

Anamorph (ANAtomic MORPHology) - The asexual form of the fungus that is recognized solely based on its anatomic morphology.

Annellide - A conidiogenous cell that gives rise to successive conidia in a basipetal manner. The apex of an annellide becomes longer and narrower as each subsequent conidium is formed and released. An apical ring composed of outer cell wall material remains as each conidium is released.

Annelloconidium (pl. annelloconidia) - A conidium formed by an annellide.

Annotation - At SGD, annotation refers to information that has been extracted from the literature and associated, on the database pages, with various aspects of an S. cerevisiae gene or chromosomal feature. SGD makes several types of annotations, such as GO, Sequence, and Literature Guide annotations.

Annular frill - A ring or skirtlike portion of cell wall material at the base of a conidium that remains when the conidium separates from its conidiophore.

Apex (pl. apices) - The tip.

Arthroconidium (pl. arthroconidia) - A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum.

Arthrospore - See arthroconidium.

Ascospore - A haploid sexual spore that is formed by free-cell formation in an ascus following karyogamy and meiosis.

Ascostroma (pl. ascostromata) - A specialized mass of hyphae containing cavities in which asci develop.

Ascus (pl. asci) - A saclike cell that gives rise to ascospore. Asci are characteristic of the Ascomycetes.

Assimilation - The utilization of nutrients for growth, with oxygen serving as the final electron acceptor.

Autolysis - The self-digestion of plant, animal, or fungal tissue.

Auxotroph - A mutant organism requiring a specific growth substance not normally required by its species.

Bacterium (pl. bacteria) - A simple prokaryotic microorganism having absorptive nutrition.

Bacteriophage - A virus that infects bacteria. The bacteriophage DNA has served as a basis for cloning vectors, and is also utilized to create phage libraries containing human or other genes.

Ballistoconidium (pl. ballistoconidia) - A forcibly discharged conidium.

Balloon form - Pertaining to a large globose conidium formed by some dermatophytes, especially Trichophyton tonsurans.

Basidiospore - A haploid sexual spore formed on a basidium following the process of karyogamy and meiosis.

Basidium (pl. basidia) - A specialized cell that gives rise to basidiospores. Basidia are characteristic of the Basidiomycetes.

Basipetal - Having the youngest conidia at the base of a chain.

Bipolar budding - The development of conidia at both ends of the parent cell.

Biseriate - Having phialides arising from metulae on the vesicles of species of Aspergillus.

Bitunicate - Having two walls.

Black yeast - A dematiaceous, unicellular, budding fungus that typically forms a black, pasty colony.

BLAST - Basic Local Alignment Search Tool is a search algorithm developed by Altschul et al. (1990). It is a very fast search algorithm that is used by the blastn, blastp, and blastx programs to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching.

Blastn - A BLAST program that compares a nucleotide query sequence against a nucleotide sequence database. The user must enter a NUCLEOTIDE sequence and select a DNA database (genoSc or GenBank) to search.

Blastp - A BLAST program that compares an amino acid query sequence against a protein sequence database. The user must submit an AMINO ACID sequence and select a PROTEIN database (NRSC) for the search.

Blastx - A BLAST program that compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. The user must enter a NUCLEOTIDE sequence and select a PROTEIN database (NRSC) for the search.

Blastoconidium (pl. blastoconidia) - A conidium that is blown out from part of its parent cell and is typically released by fission through a thickened basal septum.

Blastospore - See blastoconidium.

Budding - Asexual formation of small, rounded outgrowths from a parent cell. These will become conidia.

Capsule - A gelatinous covering around a cell.

Carry-over - Indigenous substances stored within the cells of inoculum, nutrients in the original culture medium, or both. These substances support growth of the test isolate in an assimilation study.

Catalyst - A substance, such as an enzyme, which alters the rate of a chemical reaction or allows it to take place under milder conditions than otherwise possible.

Centromere - The specialized region of a chromosome to which spindle fibers are attached, and which therefore always segregates at the first meiotic division.

Chlamydoconidium (pl. chlamydoconidia) - A rounded, enlarged conidium that usually has a thickened cell wall and functions as a survival propagule.

Chlamydospore - See chlamydoconidium.

Chromatid - One of two duplicated subunits of a chromosomes, joined at the centromere.

Chromosome - A structure composed of protein and DNA containing the nuclear genetic material of an organism.

Clone - The asexually produced progeny of an individual. To cause to grow as a clone.

Complementation - Interaction between two allelic or nonallelic genes resulting in a product or function that neither is capable of producing alone.

Circinate - Coiled into a complete or partial ring.

Clamp connection - A specialized hyphal bridge involved with nuclear division in the Basidiomycetes.

Clavate - Club shaped.

Cleistothecium (pl. cleistothecia) - An enclosed fruiting body that contains randomly dispersed asci.

ClustalW - Clustal W is an alignment program for DNA and proteins with improved sensitivity for the alignment of divergent protein sequences.

Codon - A sequence of three adjacent nucleotides that designates a specific amino acid or start/stop site for transcription.

Collarette - A small collar.

Columella (pl. columellae) - A sterile dome-like expansion at the apex of a sporangiophore.

Conical - Cone shaped.

Conidiogenous cell - A cell that gives rise to conidia.

Conidiophore - A specialized hypha upon which conidia develop.

Conidium (pl. conidia) - An asexual, non-motile, usually deciduous propagule that is not formed by cytoplasmic cleave, free-cell formation, or by conjugation.

Consensus sequence - A single sequence delineated from an alignment of multiple constituent sequences that represents a "best fit" for all those sequences. A "voting" or other selection procedure is used to determine which residue (nucleotide or amino acid) is placed at a given position in the event that not all of the constituent sequences have the identical residue at that position.

Conjugation - Sexual reproduction; fusion of gametes, in which the nuclei fuse, to produce a zygote.

Contig - A length of contiguous sequence assembled from partial, overlapping sequences, generated from a "shotgun" sequencing project. Contigs are typically created computationally, by comparing the overlapping ends of several sequencing reads generated by restriction enzyme digestion of a segment of genomic DNA. The creation of contigs in the presence of sequencing errors, ambiguities and the presence of repeats is one of the most computationally challenging aspects of the role of Bioinformatics in genome analysis.

Convergence - The end-point of any algorithm that uses iteration or recursion to guide a series of data processing steps. An algorithm is usually said to have reached convergence when the difference between the computed and observed steps falls below a pre-defined threshold.

Cosmids - DNA vectors that allow the insertion of long fragments of DNA (up to 50 kbases).

crossing over - The reciprocal exchange of chromatid segments during meiosis or mitosis.

Crosswall - A septum.

Cryptococcus neoformans - A basidiomycetous species of yeast, which can be an opportunistic pathogen, causing a life-threatening meningitis.

Culture - A population of microorganisms growing under artificial conditions.

Data Cleaning - A process whereby automated or semi-automated algorithms are used to process experimental data, including noise, experimental errors and other artifacts, in order to generate and store high-quality data for use in subsequent analysis. Data cleaning is typically required in high-throughput sequencing where compression or other experimental artifacts limit the amount of sequence data generated from each sequencing run or "read."

Data Mining - The ability to query very large databases in order to satisfy a hypothesis ("top-down" data mining); or to interrogate a database in order to generate new hypotheses based on rigorous statistical correlations ("bottom-up" data mining).

Data Processing - Data processing is defined as the systematic performance of operations upon data such as handling, merging, sorting, and computing. The semantic content of the original data should not be changed, but the semantic content of the processed data may be changed.

Data Warehouses - Vast arrays of heterogeneous (biological) data, stored within a single logical data repository, that are accessible to different querying and manipulation methods.

Database - Any file system by which data gets stored following a logical process. (see also relational database)
Deconvolution:Mathematical procedure to separate out the overlapping effects of molecules such as mixtures of compounds in a high-throughput screen, or mixtures of cDNAs in a high density array.

Dendrogram - A graphical procedure for representing the output of a hierarchical clustering method. A dendrogram is strictly defined as a binary tree with a distinguished root, that has all the data items at its leaves. Conventionally, all the leaves are shown at the same level of the drawing. The ordering of the leaves is arbitrary, as is their horizontal position. The heights of the internal nodes may be arbitrary, or may be related to the metric information used to form the clustering.

Dematiaceous - Having brown to black conidia or hyphae.

Denticle - A peg.

Dermatophyte - A fungus in the genus Epidermophyton, Microsporum, or Trichophyton that infects hair, nail, or skin.

Dimorphic - Having two different morphologic forms.

Disjunctor cell - A cell that releases a lysis.

Double septum - A thickened septum that releases a conidium by its fragmentation or separates through its center .

DNA (deoxyribonucleic acid) - The primary genetic material of all cellular organisms. It is a polymeric macromolecule composed of a repeating backbone of phosphate and sugar subunits to which different bases are attached. DNA is arranged in two opposing strands (the Watson-Crick double helix) in which the complementary bases form hydrogen-bonded basepairs across the two strands. The sugar backbone of DNA is composed of deoxyribose subunits.

DNA fingerprinting - A technique for identifying human individuals based on a restriction enzyme digest of tandemly repeated DNA sequences that are scattered throughout the human genome, but are unique to each individual.

DNA microarrays - The deposition of oligonucleotides or cDNAs onto an inert substrate such as glass or silicon. Thousands of molecules may be organized spatially into a high-density matrix. These DNA chips may be probed to allow expression monitoring of many thousands of genes simultaneously. Uses include study of polymorphisms in genes, de novo sequencing or molecular diagnosis of disease.

DNA polymerase - An enzyme that catalyzes the synthesis of DNA from a DNA template given the deoxyribonucleotide precursors.

DNA probes - Short single stranded DNA molecules of specific base sequence, labeled either radioactively or immunologically, that are used to detect and identify the complementary base sequence in a gene or genome by hybridizing specifically to that gene or sequence.

Domain (protein) - A region of special biological interest within a single protein sequence. However, a domain may also be defined as a region within the three-dimensional structure of a protein that may encompass regions of several distinct protein sequences that accomplishes a specific function. A domain class is a group of domains that share a common set of well-defined properties or characteristics.

EC number - The number assigned by the Enzyme Commission for a particular enzyme activity. Currently, SGD contains EC assignments to individual proteins, made by UniProtKB/Swiss-Prot curators. EC numbers assigned to individual proteins are displayed in the "External Classifications" section of Protein Information pages, and protein-specific links to the Enzyme nomenclature database are listed in the external links sections of both the Locus Summary and Protein Information pages. These assignments are also included in the dbxref.tab file on our FTP site.

Echinulate - Having a delicate, spiny wall.

Electronic Northerns - The use of an electronic database of cDNA sequences (or probes derived from them) in order to measure the relative levels of mRNAs expressed in different cells or tissues. An example of the use of an electronic Northern might be to identify the differences in the genes expressed in prostate cancer and those in benign prostate hyperplasia, by subtracting the database of one from the other and seeing which cDNAs remain.

Electrophoresis - The use of an external electric field to separate large biomolecules on the basis of their charge by running them through acrylamide or agarose gels.

Endemic fungus (or endemic pathogen) - The endemic fungi are those fungi able to produce an invasive infection (infection of tissue) in healthy individuals. That is, the fungus is sufficiently virulent that it does not require any help breaching the host's immune defenses. The classic endemic fungi are Cryptococcus, Histoplasma, Blastomyces, and Sporothrix. Compare with opportunistic fungus.

Endospore - A spore formed within a spherule by a cleavage process following karyogamy and mitosis.

EMBL - European Molecular Biology Labs. The EMBL Nucleotide Sequence database is a comprehensive database of DNA and RNA sequences. The database is produced in collaboration with GenBank and the DNA Database of Japan (DDBJ).

Enhancers - DNA sequences that can greatly increase the transcription rates of genes even though they may be far upstream or downstream from the promoter they stimulate.

Entrez - The Entrez Search System was developed by NCBI. Entrez allows you to retrieve molecular biology data and bibliographic citations from integrated nucleotide (GenBank, DDBJ, EMBL), protein (Swiss-Prot, PIR, PRF, PDB), and bibliographic (PubMed) databases. Within SGD database pages, external links are provided to one or more of these databases.

Enzyme - A class of proteins that are capable of catalyzing chemical reactions (the making or breaking of chemical bonds). They do so by orienting their substrates into a suitable geometry in a particular location (the active site) where electrophilic or nucleophilic amino acid residues can participate in the reaction. Enzymes are protein catalyst that speeds up chemical reactions that would otherwise be prohibitively slow under physiological conditions.

Epigenomics - The study of complex expression networks or linkages both spatially (within the body) and temporally (at different times in development).

Epistasis - A type of genetic interaction: the nonreciprocal interaction of nonallelic genes in which the expression of one gene masks the expression of another. For example, if the expression of Gene A masks that of Gene B, Gene A is said to be epistatic to Gene B, whereas Gene B is hypostatic to Gene A.

Equilibrium constant - Value that describes the equilibrium state of the reversible reaction between two molecular species

Eukaryote - An organism whose genetic information is, in contrast to prokaryotes (such as bacteria), contained in a separate cellular compartment: the nucleus. Besides algae, fungi and protozoa, all multicellular, cell-differentiating organisms including plants and animals are eukaryotes. In addition to their nuclear genome, all eukaryotic cells contain small additional, extranuclear genomes, which are contained in mitochondria (in all eukaryotes) and in plastids (only in eukaryotes that can perform photosynthesis).

Excision repair - A system of repairing single-strand damage in DNA, involving several enzymes, which first remove the damaged portion and then fill the gap by copying the remaining strand. Can operate in the dark.

Exudate - Droplets of fluid formed on the surface of a colony.

Exon - A portion of a split gene that is included in the transcript of a gene and survives processing of the RNA to become part of the spliced messenger of a structural RNA. Exons generally occupy three distinct regions of genes that encode proteins. Exons in the first region are not translated into protein, but signal the beginning of RNA transcription and contain sequences that direct the mRNA to ribosomes for protein synthesis. Exons in the second region contain the information that is translated into the amino acid sequence of the protein, and are sometimes referred to as coding exons. Exons in the third region are transcribed into the part of the mRNA that contains the signals for the termination of translation and for the addition of a polyadenylate tail.

Expressed Sequence Tags (ESTs) - A small sequence from an expressed gene that can be amplified by PCR. ESTs act as physical markers for cloning and full length sequencing of the cDNAs of expressed genes. Typically identified by purifying mRNAs, converting to cDNAs, and then sequencing a portion of the cDNAs.

Expression (gene or protein) - A measure of the presence, amount, and time-course of one or more gene products in a particular cell or tissue. Expression studies are typically performed at the RNA (mRNA) or protein level in order to determine the number, type, and level of genes that may be up-regulated or down-regulated during a cellular process, in response to an external stimulus, or in sickness or disease. Gene chips and proteomics now allow the study of expression profiles of sets of genes or even entire genomes.

Expression profile - The level and duration of expression of one or more genes, selected from a particular cell or tissue type, generally obtained by a variety of high-throughput methods, such as sample sequencing, serial analysis, or microarray-based detection.

Expression vector - A cloning vector that is engineered to allow the expression of protein from a cDNA. The expression vector provides an appropriate promoter and restriction sites that allow insertion of cDNA.

Expect threshold - The Expect threshold ("E") is a BLAST parameter that reflects the number of matches expected to be found by chance. If the statistical significance of a match is greater than the Expect threshold, the match will not be reported. Decreasing the E threshold will increase the stringency of the search: fewer matches will be reported. On the other hand, increasing the E threshold will decrease the stringency of the search and result in more matches being reported.The E threshold default is set to 10 specifically for the SGD WU-BLAST tool. The E-value cut off used for other resources and tools at SGD is documented in their respective help pages.

External Transcribed Spacer (ETS) - The ETS is a region of DNA in the rDNA repeat which flanks the 18S-5.8S-25S gene cluster and is included as part of its transcription unit. The 5' ETS is immediately upstream of the 18S gene and includes the A0 processing site. The 3' ETS is immediately downstream of the 25S gene.

Favic chandelier - A repeatedly branched cluster of hyphal apices that resembles a chandelier.

Fermentation - The ability to utilize nutrients for growth, with organic compounds serving as the final electron acceptor.

Fingerprint - A fingerprint is a set of motifs used to predict the occurrence of similar motifs, in either an individual sequence or in a database. Fingerprints are refined by iterative scanning of a composite protein sequence database. A composite or multiple-motif fingerprint contains a number of aligned motifs taken from different parts of a multiple alignment. True family members are then easy to identify by virtue of possessing all elements of the fingerprint, while subfamily members may be identified by possessing only part of it.

Filament - A threadlike element of a bacterium; a hypha of a fungus.

Fission - To split into two portions or cells.

Fission arthroconidium - An arthroconidium that is released by f1ssion through a double septum.

Floccose - Having a cottony texture.

Foot cell - The base of a macrophialoconidium produced by a species of Fusarium having a heel-like projection; the base of the conidiophore of Aspergillus species where it merges with the hypha and resembles the heel and toes of a foot.

Fragmentation - Separation of a hyphae into conidia.

Frameshift - A deletion, substitution, or duplication of one or more bases that causes the reading-frame of a structural gene to shift from the normal series of triplets.

Fungus (pl. fungi) - A eukaryotic, unicellular to filamentous, achlorophyllous organism having an absorptive nutrition. A fungus reproduces by sexual, asexual, or both means.

Functional genomics - The use of genomic information to delineate protein structure, function, pathways and networks. Function may be determined by "knocking out" or "knocking in" expressed genes in model organisms such as worm, fruitfly, yeast or mouse.

Fusiform - Tapering at both ends; spindle shaped.

Fusion protein - The protein resulting from the genetic joining and expression of 2 different genes

Gamete - Differentiated reproductive cells, generally haploid.

Gene - A section of DNA coding for a single polypeptide chain; a particular species of tRNA, snRNA or rRNA; or a sequence that is recognized by and interacts with regulator proteins.

Genome - The total set of genes of any organism.

Geniculate - Bent like a series of knees.

Germ pore - An unthickened spot in a spore or conidial wall through which a germ tube may form.

Germ tube - A hypha initially developing from a conidium or spore.

Glabrous - Smooth.

Globose - Round.

Germ line - Reproductive cells that form the gametes which carry genetic information to the next generation.
Germination : Initiation of growth by a spore.

GCG - The Genetics Computer Group is a private company involved in the development of sequence analysis software.

GenBank - GenBank is the DNA sequence database sponsored by the US National Institutes of Health. GenBank is produced in collaboration with EMBL and DDBJ. There is also a searchable DNA sequence database maintained by SGD (Yeast GenBank) that contains the subset of DNA sequences submitted to GenBank that have been derived from S. cerevisiae DNA. It includes results of the systematic sequencing as well as results from individual laboratories.

Gene - The definition of a gene changes as more properties are revealed. Two classes are generally recognized: (1) genes that are transcribed into mRNAs, which enter ribosomes and are translated into polypeptide chains, and (2) genes whose transcripts are used directly (tRNAs, rRNAs, snRNAs, etc.). Class I genes are also known as structural genes, and have been referred to as cistrons in earlier literature. There are also other shorter DNA segments that are not transcribed but instead serve as recognition sites for enzymes and other proteins that function during replication or transcription. These types of elements are generally referred to as regulatory sequences, and should not be confused with regulatory genes, which encode proteins that bind to regulatory sequences.

Gene_Info - The guide to the literature formerly called Gene_Info is now called the Literature Guide.

Gene Ontology (GO) - The Gene Ontology (GO) project was established to provide a common language to describe aspects of a gene product's biology. The use of a consistent vocabulary allows genes from different species to be compared based on their GO annotations. For each of three categories of biological information--molecular function, biological process, and cellular component--a set of terms has been selected and organized. Each set of terms uses a controlled vocabulary, and parent-child relationships between terms are defined. This combination of a controlled vocabulary with defined relationships between items is referred to as an ontology. Within an ontology, a child may be a "part of" or an example ("instance") of its parent. There are three independently organized controlled vocabularies, or gene ontologies, one for molecular function, one for biological process, and one for cellular component. Many-to-many parent-child relationships allowed in the ontologies. A gene may be annotated to any level in an ontology, and to more than one item within an ontology. The Gene Ontology project is a collaboration between three model organism databases, FlyBase (Drosophila), Saccharomyces Genome Database (SGD) and Mouse Genome Informatics (MGI).

Genetic Position - This term refers to the genetic distance between the gene and the centromere, as derived from two-point data, and is expressed in centiMorgans (cM). Locations to the left of the centromere are represented as negative numbers, and locations to the right of the centromere are represented as positive numbers. For example, GCN4/YEL009C has a genetic position of -3 cM. This means the gene is 3 cM (also called map units) to the left of the centromere (on the left arm of the chromosome). TRP2/YER090W has a genetic position of 76 cM. This means it is 76 cM (map units) to the right of the centromere (on the right arm of the chromosome). Early yeast geneticists denoted the shorter arm of each chromosome, in terms of genetic distance, as the left arm and the longer arm as the right arm. However, later physical mapping efforts and sequencing of the genome showed that for some chromosomes, the arm historically called "left" is physically longer than the "right" arm. The Combined Physical and Genetic Maps correlate physical distance (kilobase pairs) with genetic distances (cM), which can vary greatly within and between chromosomes.

Hemispheric - Half of a sphere.

Hilum (pl. hila) - A scar at the base of a conidium.

Hülle cell - A cell having a thickened cell wall and a small lumen. Hulle cells are associated with species of Aspergillus.

Hyaline - Without color.

Hypha (pl. hyphae) - An individual filament of a fungus.

Hairpin - A double-helical region in a single DNA or RNA strand formed by the hydrogen-bonding between adjacent inverse complementary sequences to form a hairpin shaped structure.

Haploid - A cell or organism containing only one set of chromsomes without the homologous pairs.

Heterodimer - Protein composed of 2 different chains or subunits.

Heteroduplex - Hybrid structure formed by the annealing of two DNA strands (or an RNA and DNA) that have sufficient complementarity in their sequence to allow hydrogen bonding.

Hidden Markov model (HMM) - A joint statistical model for an ordered sequence of variables. The result of stochastically perturbing the variables in a Markov chain (the original variables are thus "hidden"), where the Markov chain has discrete variables which select the "state" of the HMM at each step. The perturbed values can be continuous and are the "outputs" of the HMM. A Hidden Markov Model is equivalently a coupled mixture model where the joint distribution over states is a Markov chain. Hidden Markov models are valuable in bioinformatics because they allow a search or alignment algorithm to be trained using unaligned or unweighted input sequences; and because they allow position-dependent scoring parameters such as gap penalties, thus more accurately modeling the consequences of evolutionary events on sequence families.

High-throughput screening - The method by which very large numbers of compounds are screened against a putative drug target in either cell-free or whole-cell assays. Typically, these screenings are carried out in 96 well plates using automated, robotic station based technologies or in higher- density array ("chip") formats.

Homology - (strict) Two or more biological species, systems or molecules that share a common evolutionary ancestor. (general) Two or more gene or protein sequences that share a significant degree of similarity, typically measured by the amount of identity (in the case of DNA), or conservative replacements (in the case of protein), that they register along their lengths. Sequence "homology" searches are typically performed with a query DNA or protein sequence to identify known genes or gene products that share significant similarity and hence might inform on the ancestry, heritage and possible function of the query gene.

Housekeeping genes - Genes that are always expressed (ie. they are said to be constitutively expressed) due to their constant requirement by the cell.

Hybridization - The interaction of complementary nucleic acid strands. This can occur between two DNA strands or between DNA and RNA strands, and is the basis of many techniques such as Southern and northern blots.

Hydrogen bond - A weak chemical interaction between an electronegative atom (e.g. nitrogen or oxygen) and a hydrogen atom that is covalently attached to another atom. This bond maintains the two-helices of DNA together and is also the primary interaction between water molecules.

Hydrophilicity - (lit. water-loving) The degree to which a molecule is soluble in water. Hydrophilicity depends to a large degree on the charge and polarizability of the molecule and its ability to form transient hydrogen-bonds with (polar) water molecules.

Hydrophobicity - (lit. water-hating) The degree to which a molecule is insoluble in water, and hence is soluble in lipids. If a molecule lacking polar groups is placed in water, it will be entropically driven to finding a hyrdophobic environment (such as the interior of a protein or a membrane).

Idiotype - Antibody variants localized to the variable portion of an immunoglobulin that are recognised by their antigenic determinants. The determinants are composed from the antigen-combining site or CDRs. Every unique antigenic determinant has a specific antibody with its own unique idiotype.

Indel - A hybrid term (combining the words "insertion" and "deletion") used to describe a difference in sequence due to either an insertion or a deletion event; especially used when the evolutionary direction of the change is unspecified.

Intercalary -Occurring within a hypha.

Internode - That portion of a hypha that is between two nodes.

Introns - Noncoding regions of eukaryotic genes, which are transcribed into mRNA but are then excised by a process called RNA-splicing.

Immunoglobulin - A member of the globulin protein family consisting of two light and two heavy chains linked by disulfide bonds. All antibodies are immunoglobulins.

in silico (biology) - (Lit. computer mediated). The use of computers to simulate, process, or analyse a biological experiment.

in situ hybridization - A variation of the DNA/RNA hybridization procedure in which the denatured DNA is in place in the cell and is then challenged with RNA or DNA extracted from another source. (See also fluorescence in situ hybridization).

Integration - The physical insertion of DNA into the host cell genome. The process is used by retroviruses where a specific enzyme catalyses the process or can occur at random sites with other DNA (eg. Transposons).

Intracellular signaling - The communication of a molecular message from the surface of the cell to the nucleus via the participation of a series of molecules, including receptors, enzymes, proteins, and small-molecules. The end result of the signalling process is the up- or down-regulation of a particular series of genes that may be involved in cell growth, division or differentiation.

Isoschizomers - Two different restriction enzymes which recognize and cut DNA at the same recognition site. e.g Sma I and Xma I both recognize and cut the sequence CCCGGG.

Isozymes - Two or more enzymes capable of catalyzing the same reaction but varying in their specificity due to differences in their structures and hence their efficiencies under different environmental conditions.

Iteration - A series of steps in an algorithm whereby the processing of data is performed repetitively until the result exceeds a particular threshold. Iteration is often used in multiple sequence alignments whereby each set of pairwise alignments are compared with every other, starting with the most similar pairs and progressing to the least similar, until there are no longer any sequence-pairs remaining to be aligned.

Junk DNA - Term used to describe the excess DNA that is present in the genome beyond that required to encode proteins. A misleading term since these regions are likely to be involved in gene regulation, and other as yet unidentified functions.

Karyotype - The constitution (typically number and size) of chromosomes in a cell or individual.

Kyoto - An external link in the Locus or Clone page to the Kyoto Encyclopedia of Genes and Genomes. The link goes directly to the information for that specific enzyme

Lageniform - Flask shaped with a tapering distal portion.

Lanose - Having a woolly texture.

Lead compound - A candidate compound identified as the best "hit" (tight binder) after screening of a combinatorial (or other) compound library, that is then taken into further rounds of screening to determine its suitability as a drug.

Lead optimization - The process of converting a putative lead compound ("hit") into a therapeutic drug with maximal activity and minimal side affects, typically using a combination of computer-based drug design, medicinal chemistry and pharmacology.

Lexicon - In Bioinformatics, a lexicon refers to a pre-defined list of terms that together completely define the contents of a particular database.

Library - A large collection of compounds, peptides, cDNAs or genes which may be screened in order to isolate cognate molecules.

Ligand - Any small molecule that binds to a protein or receptor; the cognate partner of many cellular proteins, enzymes, and receptors.

linkage - Failure of genes to segregate independently because they reside on the same chromosome.

Linkage map - A genetic map of a chromosome or genome delineated by mapping the positions of genes to their chromosomes by their linkage to readily identifiable genetic loci.

locus - The position on a chromosome occupied by a gene.

Long Terminal Repeat (LTR) - Identical sequences, typically several hundred nucleotides in length, that are located both at the ends of intact Ty retrotransposons and as solo elements present in multiple copies throughout the genome. There are several types of LTR elements in yeast: delta, tau, sigma and omega.

Lysis - Dissolution.

Macroconidium (pl. macroconidia) - The larger of two conidia of two different sizes that are produced in the same manner by a single fungus.

Map unit - A measure of genetic distance between two linked genes that corresponds to a recombination frequency of 1%.

Markov chain - Any multivariate probability density whose independence diagram is a chain.The variables are ordered, and each variable "depends" only on its neighbors in the sense of being conditionally independent of the others. Markov chains are an integral component of hidden Markov models.

Mating type - The sex of a yeast cell. In S. cerevisiae three types of cells can be distinguished: a, alpha and a/alpha. The haploid a and alpha cells can mate with each other. During mating, cellular and nuclear fusion of the two cells of opposite mating type occurs, forming the third cell type, the diploid a/alpha cell. The a/alpha cell cannot mate but, unlike a and alpha cells, can be induced by external signals to enter meiosis and undergo sporulation.

Merosporangium (pl. merosporangia) - A sporangium having its sporangiospores in a single row.

Metula (pl. metulae) - A sterile branch upon which phialides of some species of Aspergillus and Penicillium develop.

Meiosis - A special process of nuclear division during which spores are produced. Meiosis involves a diminution (by half) in the amount of genetic material; it consists of two successive nuclear divisions with only one round of DNA replication producing four haploid daughter cells (the spores) from an initial diploid cell.

Melting (of DNA) - The denaturation of double-stranded DNA into two single strands by the application of heat. (Denaturation breaks the hydrogen bonds holding the double-stranded DNA together).

Messenger RNA (mRNA) - The complementary RNA copy of DNA formed from a single-stranded DNA template during transcription that migrates from the nucleus to the cytoplasm where it is processed into a sequence carrying the information to code for a polypeptide domain.

Methylation - The addition of -CH3 (methyl) groups to a target site. Typically such addition occurs on to the cytosine bases of DNA.

Microarray - A 2D array, typically on a glass, filter, or silicon wafer, upon which genes or gene fragments are deposited or synthesized in a predetermined spatial order allowing them to be made available as probes in a high-throughput, parallel manner.

Microconidium (pl. microconidia) -The smaller of two conidia of two different sizes that are produced in the same manner by a single fungus.

Mitochondria - Semi-autonomous, self-reproducing organelles within the cytoplasm of eukaryotic cells that are bounded by two membranes. These organelles are responsible for the energy conversion of most of the cellular energy metabolites into adenosine triphosphate (ATP) by oxidative phosphorylation.

Microfluidics - The miniaturization of chemical reactions or pharmacalogical assays into microscopic tubes or vessels in order to greatly increase their throughput, by placing many of them side-by-side in an array.

Mimetics - Compounds that mimic the function of other molecules via their high degree of structural (conformational) similarity, and hence physio-chemical properties.

Missense mutation - A point mutation in which one codon (triplet of bases) is changed into another designating a different amino acid.

Mitosis - The nuclear division that results in the replication of the genetic material and its redistribution into each of the daughter cells during cell division.

Modeling - In bioinformatics, modeling usually refers to molecular modeling, a process whereby the three-dimensional architecture of biological molecules is interpreted (or predicted), visually represented, and manipulated in order to determine their molecular properties. (general) A series of mathematical equations or procedures which simulate a real-life process, given a set of assumptions, boundary parameters, and initial conditions.

Monomer - A single unit of any biological molecule or macromolecule, such as an amino acid, nucleic acid, polypeptide domain, or protein.

Monovalent - Having one binding site; strictly, an atom with only one free electron available for binding in its highest energy shell.

Motif - A conserved element of a protein sequence alignment that usually correlates with a particular function. Motifs are generated from a local multiple protein sequence alignment corresponding to a region whose function or structure is known. It is sufficient that it is conserved, and is hence likely to be predictive of any subsequent occurrence of such a structural/functional region in any other novel protein sequence.

Moniliform - Having swellings.

Morphology - The form and structure of an organism.

Mould - A filamentous fungus.

Multiple budding - The development of several series of blastoconidia around a parent yeast cell.

Muriform - Having vertical and horizontal septa.

Multigene family - A set of genes derived by duplication of an ancestral gene, followed by independent mutational events resulting in a series of independent genes either clustered together on a chromosome or dispersed throughout the genome.

Multiple (sequence) alignment - A Multiple Alignment of k sequences is a rectangular array, consisting of characters taken from the alphabet A, that satisfies the following conditions: There are exactly k rows; ignoring the gap character, row number i is exactly the sequence sI; and each column contains at least one character different from "-". In practice multiple sequence alignments include a cost/weight function, that defines the penalty for the insertion of gaps (the "-" character) and weights identities and conservative substitutions accordingly. Multiple alignment algorithms attempt to create the optimal alignment defined as the one with the lowest cost/weight score.

Multiplex sequencing - Approach to high-throughput sequencing that uses several pooled DNA samples run through gels simultaneously and then separated and analyzed.

Mutagen - Any agent that can cause an increase in the rate of mutations in an organism.

Mutation - An inheritable alteration to the genome that includes genetic (point or single base) changes, or larger scale alterations such as chromosomal deletions or rearrangements.

Mycelia sterilia - See Sterile Hyphae.

Mycelium - The aggregated mass of hyphae making up a fungus.

Mycology - The branch of biology that deals with the study of fungi.

MV medium: A chemically defined minimal growth medium for yeast supplemented with vitamins.

Medline - Medline is the National Library of Medicine's database of biomedical papers; it contains all citation information for each paper, as well as abstracts for most of the papers.

Medline UID - The "Medline" tag that appears within the listed information for a paper contains the Medline unique identifying number (UID) for the paper; the first 2 numbers usually (but not always) indicate the year of publication.

Merged Feature - A chromosomal feature that was once annotated as a distinct entity, but that has now been subsumed by another feature. Typically, features become "Merged" because of a change in chromosomal sequence or annotation (e.g. YAR004W). For record keeping, the "Merged" feature is not removed from SGD, but is instead given the "Merged" status as a flag.

Minimal Tiling Path - A map or table showing placement and order of a set of clones that completely, contiguously cover some segment of DNA in which you are interested.

MIPS - The initials stand for Munich Information Center for Protein Sequences. MIPS is the coordinator of the European Commission Genome Projects.

Molecular Function - One of the three categories used by the Gene Ontology project, molecular function describes the tasks performed by individual gene products; examples are transcription factor and DNA binding.

Node - Where a stolon touches a surface.

Nodular organ - A knot of hyphae that is often produced by dermatophytes.

Nomen confusum (nom. conf.) - A name based on two or more different components.

Nomen conservandum (nom. cons.) - A name authorized for use by the International Botanical Congress (IBC).

Nomen dubium (nom. dub.) - A name of uncertain sense.

Nomen illegitimum (nom. illegit.) - A validly published name, but one that contravenes some of the articles of the IBC.

Nomen invalidum (nom. inval.) - A name that is not valid

Nomen nudum (nom. nud.) - A name that lacks a description.

Northern blotting - A technique to identify RNA molecules by hybridization that is analogous to Southern blotting (see Southern blotting).

Nuclease - Any enzyme that can cleave the phosphodiester bonds of nucleic acid backbones.

Nucleoside - A five-carbon sugar covalently attached to a nitrogen base.

Nucleotide - A nucleic acid unit composed of a five carbon sugar joined to a phosphate group and a nitrogen base.

NCBI - The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) in the National Institutes of Health (NIH). Its mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. NCBI developed and maintains the Entrez Search System and PubMed database.

NiceZyme - An external link on the Locus or Clone page) to the Enzyme nomenclature database maintained by SwissProt. The link goes directly to the information for that specific enzyme.

Nomenclature Note - This note is used by SGD on the locus page to clarify gene naming issues like two different ORFs being referred by the same gene name in the literature.

Nontranscribed Spacer (NTS) - The NTS is a region of DNA flanking the 5S rRNA gene within the ribosomal DNA repeat. NTS1 lies between the 25S and 5S genes, and NTS2 lies between the 5S and 18S genes. Note that NTS regions are not included in the 35S pre-rRNA transcript, and the 5S gene is transcribed independently of the other rRNA genes and in the opposing direction.

Obclavate - Club shaped in reverse.

Obovoid - Egg shaped in reverse.

Obsolete - A synonym of a published name that is no longer acceptable for use. Possible reasons for being invalid are coded as nom. conf., nom. dub., nom. illegit., or nom. nud.

Olivaceous - Having an olive shade of color.

Ostiolate - Having an ostiole.

Ostiole - A mouth or opening through which spores or conidia may escape.

Oval - Egg-shaped.
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Oligonucleotide - A short molecule consisting of several linked nucleotides (typically between 10 and 60) covalently attached by phosphodiester bonds.

Open reading frame (ORF) - Any stretch of DNA that potentially encodes a protein. Open reading frames start with a start codon, and end with a termination codon. No termination codons may be present internally. The identification of an ORF is the first indication that a segment of DNA may be part of a functional gene.

Operator - A segment of DNA that interacts with the products of regulatory genes and facilitates the transcription of one or more structural genes.

Operon - A unit of transcription consisting of one or more structural genes, an operator, and a promoter.

Ortholog - Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution. Identification of orthologs is critical for reliable prediction of gene function in newly sequenced genomes.

Overlapping clones - Collection of cloned sequences made by generating randomly overlapping DNA fragments with infrequently cutting restriction enzymes.

opportunistic pathogen - An organism which, although not normally disease-causing, can cause disease in individuals whose resistance has been weakened in some way.

organelle - A cell substructure.

oxidative metabolism - Energy-releasing processes which require free oxygen.

Papilla (pl. papillae) - A small nipple-shaped elevation.

Penicillus - A brush-like conidial bead produced by members of the genus Penicillium.

Percurrent - Developing through a previous apex.

Perforating organ - A mass of hyphae producing a conical cavity in the in vitro hair test; a characteristic property of certain keratinophilic fungi.

Perithecium (pl. perithecia) - A fruiting body having asci in a basal group or as a layer; perithecia are usually flask shaped, with an opening through which the asci or ascospore escape.

Phialide - A type of conidiogenous cell that gives rise to successive conidia from a fixed site in a basipetal manner. A phialide does not increase in length as the conidia are formed, and its apex does not become smaller in diameter. A collarette is often present at the apex of the phialide.

Phialoconidium (pl. phialoconidia) - A conidium produced by a phialide.

Phycomycetes - An archaic class name once used for the lower fungi in general. These organisms are now placed either in the kingdom Protista or in the classes Trichomycetes and Zygomycetes of the kingdom Fungi.

Pleomorphic - Having several forms. The term is also applied to dermatophyte colonies that become irreversibly sterile.

Polymorphic - Having several forms.

Poroconidium (pl. poroconidia) - A conidium that forms through a pore in the cell wall of its conidiogenous cell.

Propagulen - A reproductive unit.

Pseudohypha (pl. pseudohyphae) - A series of blastoconidia that have remained attached to each other forming a filament. The blastoconidia are often elongated with the points of attachment between adjacent cells being constricted.

Pseudomycelium - A large amount of pseudohyphae.

Pycnidium (pl. pycnidia) - A sac-like fruiting body that gives rise to conidia within its central area.

Pyriform - Pear shaped.

Palindrome - A region of DNA with a symmetrical arrangement of bases occuring about a single point such that the base sequences on either side of that point are identical (if the strands are both read in the same direction) e.g 5í GAATTC 3í whose complementary sequence is 3í CTTAAG 5í.

Pattern - Molecular biological patterns usually occur at the level of the characters making up the gene or protein sequence. A pattern language must be defined in order to apply different criteria to different positions of a sequence. In order to have position-specific comparison done by a computer, a pattern-matching algorithm must allow alternative residues at a given position, repetitions of a residue, exclusion of alternative residues, weighting, and ideally, combinatorial representation.

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Paralog - Paralogs are genes related by duplication within a genome. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one.

Parameters - Parameters are user-selectable values, typically experimentally determined, that govern the boundaries of an algorithm or program. For instance, selection of the appropriate input parameters governs the success of a search algorithm. Some of the most common search parameters in bioinformatics tools include the stringency of an alignment search tool, and the weights (penalties) provided for mismatches and gaps.

Peptide - A short stretch of amino acids each covalently coupled by a peptide (amide) bond.

Peptide bond (amide bond) - A covalent bond formed between two amino acids when the amino group of one is linked to the carboxy group of another (resulting in the elimination of one water molecule).

Phage (Bacteriophage) - A virus that infects bacterial cells and serves as a useful vector for introducing genes into bacteria for a number of purposes.

Pharmacogenomics - The use of (DNA-based) genotyping in order to target pharmaceutical agents to specific patient populations. Genetic differences are known to affect responses to many types of drug therapy, and pharmacogenomics analysis serves to customize the use of pharmaceuticals for specific subgroups of patients.The rationale for this approach is that observed gene expression differences may correlate with, and explain, the differences in side effects and efficacy to drugs in humans.

Pharmacophore - The three dimensional spatial arrangment of atoms, substituents, functional groups, or chemical features that together are sufficient to describe the pharmacologically active components of a drug molecule or molecule series.

Phenotype - Any observable feature of an organism that is the result of one or more genes.

Physical map - A physical map consists of a linearly ordered set of DNA fragments encompassing the genome or region of interest. Physical maps are of two types, macro-restriction maps and ordered clone maps. The former consists of an ordered set of large DNA fragments generated by using restriction enzymes whose recognition sequences are infrequently represented in the genome. An ordered clone map consists of an overlapping collection of cloned DNA fragments. The DNA may be cloned into any one of the available vector systems--YACs, cosmids, phage, or even plasmids. Major advantages of ordered clonemaps are that they are of high resolution and directly provide the clones for further study.

Plasmid - Any replicating DNA element that can exist in the cell independently of the chromosomes. Synthetic plasmids are used for DNA cloning. Most commonly found in bacterial cells.

Pleitropy - The multiple effects on an organismís phenotype due to a single gene or allele e.g the cytokines which can bind to multiple cellular receptors and effect growth and multiple immune pathways.

Point mutation - A mutation in which a single nucleotide in a DNA sequence is substituted by another nucleotide.

Poly(A) tail - The stretch of Adenine (A) residues at the 3í end of eukaryotic mRNA that is added to the pre-mRNA as it is processed, before its transport from the nucleus to the cytoplasm and subsequent translation at the ribosome.

Polyadenylation site - A site on the 3í-end of messenger RNA (mRNA) that signals the addition of a series of Adenines during the RNA processing step and before the mRNA migrates to the cytoplasm. These so-called poly(A) "tails" increase mRNA stability andallow one to isolate mRNA from cells by PCR-amplification using poly(T) primers.

Polymorphism - (lit. many forms) The existence of a gene in a population in at least two different forms at a frequency far higher than that attributable to recurrent mutation alone. Variations in a population may be measured by determining the rate of mutation in polymorphic genes (see SNPs).

Polypeptide - A single chain of covalently attached amino acids joined by peptide bonds. Polypeptide chains usually fold into a compact, stable form (a domain) that is part (or all) of the final protein.

Primer - A short oligonucleotide that provides a free 3í hydroxyl for DNA or RNA synthesis by the appropriate polymerase (DNA polymerase or RNA polymerase).

Probe - Any biochemical that is labelled or tagged in some way so that it can be used to identify or isolate a gene, RNA, or protein.

Profile - Sequence profiles are usually derived from multiple alignments of sequences with a known relationship, and consist of tables of position-specific scores and gap-penalties. Each position in the profile contains scores for all of the possible amino acids, as well as one penalty score for opening and one for continuing a gap at the specified position. Attempts have been made to further improve the sensitivity of the profile by refining the procedures to construct a profile starting from a given multiple alignment. Other representations for sequence domains or motifs do not necessarily require the presence of a correct and complete multiple alignment, such as hidden Markov models.

Prokaryote - An organism or cell that lacks a membrane-bounded nucleus. Bacteria and blue-green algae are the only surviving prokaryotes (cf. Eukaryote).

Promoter (site) - A promoter site is defined by its recognition by eukaryotic RNA polymerase II; its activity in a higher eukaryote; by experimentally evidence, or homology and sufficient similarity to an experimentally defined promoter; and by observed biological function.

Protein families - Sets of proteins that share a common evolutionary origin reflected by their relatedness in function which is usually reflected by similarities in sequence, or in primary, secondary or tertiary structure. Subsets of proteins with related structure and function.

Proteome - The entire protein complement of a given organism.

Proteomics - The study of the proteome. Typically, the cataloging of all the expressed proteins in a particular cell or tissue type, obtained by identifying the proteins from cell extracts using a combination of 2D gel electrophoresis and mass spectrometry. The large scale analysis of the protein composition and function. (cf genomics)

Purine - A nitrogen-containing compound with a double-ring structure. The parent compound of Adenine and Guanine.

Pyrimidine - A nitrogen-containing compound with a single six-membered ring structure. The parent compound of Thymidine and Cytosine.

Prasexual cycle - A series of events leading to genetic recombination in vegetative or somatic cells.

Peptide- A short chain of chemically bonded amino acids.

Petite colony mutation ("petites") - Respiration deficient variants of yeast resulting from lack of or defective mitochondria.

PETITE medium - A yeast growth medium containing yeast extract and glycerol, used to distinguish petite colony mutants, which cannot assimilate glycerol.

Phenotype - The expression of the genotype in the appearance and functions of an organism; the observable traits.

P-value - In a BLAST search, a P-value refers to the probability of obtaining, by chance, a pairwise sequence comparison of the observed similarity given the length of the query sequence and size of the database searched. Thus, low P-values indicate sequence similarities of high significance.

PAM120 - Sequence alignment matrix that allows 120 accepted point mutations per 100 amino acids. A higher PAM is more suitable for comparing distantly related sequences, while a lower PAM is suitable for comparing closely related sequences (Swartz and Dayhoff, 1978).

PAM250 - Sequence alignment matrix that allows 250 accepted point mutations per 100 amino acids. PAM250 is suitable for comparing distantly related sequences, while a lower PAM is suitable for comparing more closely related sequences (Swartz and Dayhoff, 1978).

PAM40 - Sequence alignment matrix that allows 40 accepted point mutations per 100 amino acids. PAM40 is sutiable for comparison of closely related sequences, while a higher PAM is suitable for comparison of more distantly related sequences (Swartz and Dayhoff, 1978).

PatMatch - This is a pattern matching program that permits the identification of patterns or motifs within the collection of all S. cerevisiae protein or DNA sequences. It offers an alternative to sequence alignment techniques such as BLAST and FASTA for identifying nucleotide or peptide sequences with conserved or biologically interesting regions.

PDB - The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, based at the Brookhaven National Laboratory.

PIR - PIR (Protein Information Resource) is a protein database whose entries for yeast proteins are incorporated into SGD. On a Locus page, the PIR link can be found under the "External Links category" and it connects directly to the PIR entry for the gene. The entry includes the amino acid sequence for the protein encoded by the gene. The PIR database has three sites, PIR-DE based in Germany, PIR-JP based in Japan, and PIR-US in the United States.

Point mutation - A single nucleotide change that substitutes one nucleotide for another. A point mutation in the coding sequence of a gene affects a single codon, and often allows expression of an intact but nonfunctional or partially functional protein.

PubMed - PubMed is a database of bibliographic information developed by NCBI.

Rachis - An extension of a conidiogenous cell-bearing conidia.

Racket hyphae (also spelled racquet) - A hypha having a series of cells that are swollen at one end.

Radiating - Spreading from a common center.

Reflexive hypha - A hypha having short branches that bend backward at approximately a 45° angle.

Rhizoid - Pertaining to a root-like group of hyphae.

Rudimentary - Poorly developed.

Reagents - Sources of biological or chemical material that can be used as the starting blocks in laboratory experiments. Reagents can range from chemicals needed to perform a particular chemical reaction, constituents of a laboratory protocol, or clones to be used in a large-scale gene expression study.

Recessive - Any trait that is expressed phenotypically only when present on both alleles of a gene (cf dominant)
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Recombinant DNA (rDNA) - DNA molecules resulting from the fusion of DNA from different sources. The technology employed for splicing DNA from different sources and for amplifying the resultant heterogenous DNA.

Recombination - A new combination of alleles resulting from the rearrangement occuring by crossing-over or by independent assortment (see crossing over).

Recursion - An algorithmic procedure whereby an algorithm calls on itself to perform a calculation until the result exceeds a threshold, in which case the algorithm exits. Recursion is a powerful procedure with which to process data and is computationally quite efficient.

Regulatory gene - A DNA sequence that functions to control the expression of other genes by producing a protein that modulates the synthesis of their products (typically by binding to the gene promoter). (cf. Structural gene).

Repressor - The protein product of a regulatory gene that combines with a specific operator (regulatory DNA sequence) and hence blocks the transcription of genes in an operon.

Restriction enzyme (restriction endonuclease) - A type of enzyme that recognizes specific DNA sequences (usually palindromic sequences 4, 6, 8 or 16 base pairs in length) and produces cuts on both strands of DNA containing those sequences only. The "molecular scissors" of rDNA technology.

Restriction fragment length polymorphisms (RFLPs) - Variation within the DNA sequences of organisms of a given species that can be identified by fragmenting the sequences using restriction enzymes, since the variation lies within the restriction site. RFLPs can be used to measure the diversity of a gene in a population.

Restriction map - A physical map or depiction of a gene (or genome) derived by ordering overlapping restriction fragments produced by digestion of the DNA with a number of restriction enzymes.

Reverse transcriptase - A DNA polymerase that can synthesise a complementary DNA (cDNA) strand using RNA as a template - a so-called RNA-dependent DNA polymerase.

Reverse transcriptase-PCR (RT-PCR) - Procedure in which PCR amplification is carried out on DNA that is first generated by the conversion of mRNA to cDNA using reverse transcriptase.

RAW format - A format in which the nucleotide sequence appears without headers or comments. RAW format must be used when performing an S. cerevisiae search in BLAST or FASTA.
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Regulatory Region - A region that is involved in controlling the expression of a gene. Regulatory regions can include, but are not limited to, transcription factor binding sites that regulate the transcription of a gene or untranslated regions that regulate the protein levels of a gene product.

Related Sequences - A feature of Entrez that finds related nucleotide (GenBank) or protein (GenPept) sequences using similarity searches.

Repeat Region - A region containing some type of tandemly repeated sequence. For example, in the case of the telomeric Y' elements, these are known as "36-bp repeats".

Retrotransposon - Transposable element that mobilizes via an RNA intermediate. Each DNA segment in the host chromosome is transcribed into RNA and then reverse-transcribed via a reverse transcriptase into a DNA segment. This is reinserted into the host genome, usually at a new site. Retroposon is a shortened form of retrotransposon, and also appears in the literature.

Sclerotium (pl. sclerotia) - An organized mass of hyphae that remains dormant during unfavorable conditions.

Septum (pl. septa) - A crosswall.

Seta (pl. setae) - A bristle or bristle-like structure.

Shield cell - A conidium having the shape of a shield. Shield cells are commonly produced by members of the genus Cladosporium.

Sinuous - Wavy.

Solitary - Separate; alone.

Spherule - A sporangium-like structure containing endospores that is produced by Coccidioides immitis or Rhinosporidium seeberi.

Sporangiolum (pl. sporangiola) - A sporangium that contains a small number of sporangiospores. Some sporangiola may contain only one sporangiospore.

Sporangiophore - A specialized hypha that gives rise to a sporangium.

Sporangiospore - A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium.

Sporangium (pl. sporangia) - An asexual sac-like cell that has its entire content cleaved into sporangiospores.

Spore - A reproductive propagule that forms either following meiosis or asexually by a cleavage process.

Sporodochium (pl. sporodochia) - A cushion-like mat of hyphae bearing conidiophores over its surface.

Sterigma (pl. sterigmata) - A pedicel bearing a basidiospore.

Sterile Hyphae - A mould that is growing only in its filamentous phase without produce conidia or other fruiting bodies. The identification of the moulds depends on seeing conidia, fruiting bodies, and other similar structures and the mould thus cannot be fully identified.

Stolon - A runner.

Subglobose - Almost round.

Submerged - Within the nutrient agar.

Sympodial - Pertaining to the growth of a conidiophore in which new successive lateral, subterminal apices of growth occur following successive conidium formation. Sympodial conidiophores are typically geniculate in appearance.

Synanamorph - Two or more distinct anatomic forms (anamorphs) produced by one fungus.

Synnema (pl. synnemata) - An erect macroscopic structure consisting of united conidiophores that bear conidia terminally, laterally, or in both ways.

Sense strand - The strand of double-stranded DNA that acts as the template strand for RNA synthesis. Typically only one gene product is produced per gene, reading from the sense strand only. (Some viruses have open reading frames in both the sense and the antisense strands).

Sequence Tagged Site (STS) - A unique sequence from a known chromosomal location that can be amplified by PCR. STSs act as physical markers for genomic mapping and cloning.

Shotgun cloning - The cloning of an entire gene segment or genome by generating a random set of fragments using restriction endonucleases to create a gene library that can be subsequently mapped and sequenced to reconstruct the entire genome.

Similarity (homology) search - Given a newly sequenced gene, there are two main approaches to the prediction of structure and function from the amino acid sequence. Homology methods are the most powerful and are based on the detection of significant extended sequence similarity to a protein of known structure, or of a sequence pattern characteristic of a protein family. Statistical methods are less successful but more general and are based on the derivation of structural preference values for single residues, pairs of residues, short oligopeptides or short sequence patterns. The transfer of structure/function information to a potentially homologous protein is straightforward when the sequence similarity is high and extended in length, but the assessment of the structural significance of sequence similarity can be difficult when sequence similarity is weak or restricted to a short region.

Signal sequence (leader sequence) - A short sequence added to the amino-terminal end of a polypeptide chain that forms an amphipathic helix allowing the nascent polypeptide to migrate through membranes such as the endoplasmic reticulum or the cell membrane. It is cleaved from the polypeptide after the protein has crossed the membrane.

Single nucleotide polymorphisms (SNPs) - Variations of single base pairs scattered throughout the human genome that serve as measures of the genetic diversity in humans. About 1 million SNPs are estimated to be present in the human genome, and SNPs are useful markers for gene mapping studies.

Southern blotting - A procedure for the identification of DNA by transmitting a fragment isolated on an agarose gel to a nitrocellulose filter where it can be hybridized with a complementary "probe" sequence.

Substitution matrix - A model of protein evolution at the sequence level resulting in the development of a set of widely used substitution matrices. These are frequently called Dayhoff, MDM (Mutation Data Matrix), BLOSUM or PAM (Percent Accepted Mutation) matrices. They are derived from global alignments of closely related sequences. Matrices for greater evolutionary distances are extrapolated from those for lesser ones.

Saccharomyces cerevisiae - Taxonomic classification: Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces. Saccharomyces is a genus of ascomycetes. They are normally diploid unicellular fungi that reproduce asexually by budding. Asci, containing four haploid ascospores, develop directly from the diploid vegetative cells by meiosis. After germination of the ascospores the haploid cells can reproduce vegetatively, or haploid cells of different mating type can fuse to form a diploid zygote. Most laboratory strains used are, in contrast to wild- type yeasts, stable haploids.

scRNA (small cytoplasmic RNA) - A set of RNAs that are typically smaller than 300 nucleotides and can be part of signal recognition particles (SRPs).

Signal recognition particles (SRPs) - Ribonucleoproteins that are part of the protein-translocating machinery in the ER (endoplasmic reticulum) membrane.

snRNA - A set of RNAs that are typically smaller than 300 nucleotides and function in the nucleus in the form of small nuclear ribonucleoprotein particles (snRNPs). The function of snRNPs is to mediate and regulate post-translational RNA processing events.

Solo LTR - A solitary LTR sequence lacking a TY element. This indicates that a TY was located in this region. As the remaining LTR has no function anymore, and on the other hand its sequence is well conserved the transposition must have occured in the near past.

Spindle - A network of fibrous microtubules and associated molecules formed during mitosis between the opposite poles (centromeres) of eukaryotic cells. It mediates the movement of the duplicated chromosomes to opposite poles.


Sporulation - The process of spore development. Sporulation can be induced by external signals, such as absence of nitrogen.

Smith-Waterman alignment - An amino acid sequence alignment that illustrates sequence similarity. The alignment is generated using the Smith-Waterman algorithm (T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197 and W.R. Pearson (1991) Genomics 11:635-650).

SwissProt - SwissProt is an annotated protein sequence database. Within a Locus page, an external link is provided (at the "SwissProt" tag) to the SwissProt entry for the gene, which includes the amino acid sequence for the protein encoded by the gene.

Synteny - Location of genes on the same chromosome, e.g., genes with a common chromosomal location are said to be part of the same syntenic group. Also used to refer to conservation of gene order across species, e.g., if orthologous genes are located together and in the same relative order in different species, then the block of genes is said to be syntenic between the species.

Teleomorph - A form based on a sexual state.

Truncate - Ending abruptly.

Tuberculate - Having finger-like or wart-like projections.

Tertiary structure - Folding of a protein chain via interactions of its sideschain molecules including formation of disulphide bonds between cysteine residues.

Transformation - A genetic alteration to a cell as a result of the incorporation of DNA from a genetically diferent cell or virus; can also refer to the introduction of DNA into bacterial cells for genetic manipulation.

Transgene - A foreign gene that is introduced into a cell or whole organism (eg.transgenic mice) for therapeutic or experimental purposes.

Translation - The process of converting RNA to protein by the assembly of a polypeptide chain from an mRNA molecule at the ribosome.

Transmembrane region - The region of a transmembrane protein that actually spans the membrane. Transmembrane regions are usually hydrophobic in order to be thermodynamically compatible with the lipid bilayer portion of the membrane. They may consist of either alpha-helical or beta-strand secondary structure elements, but in either case the external residues (the ones facing the membrane) are invariably hydrophobic while the internal residues may be hydrophilic (as in the case of a pore or channel) or polar. One common transmembrane structural domain is the seven-helix bundle seen in numerous channel proteins.

Telomere - The terminal part of a eukaryotic chromosome, consisting of a few hundred base pairs with a defined structure. Telomeres are important for maintaining chromosomal structure and stability, as they permit replication of the ends of the linear DNA molecule.

Transcription - The process by which DNA is used as a template for the synthesis of an RNA molecule.

Translation - The process of protein synthesis from a mRNA template, occurring at the ribosome.

Transposable element (transposon) - A mobile DNA sequence that can move from one site in a chromosome to another, or between different chromosomes. The transposable elements in yeast are the TY elements.

TY elements - The retrotransposons of yeast. TYs are members of a widely distributed family of eukaryotic elements called LTR- containing retrotransposons. They have the same sequence organization as retroviruses. The complete retrotransposons are 5 to 6 kilobases long. They are bracketed by long terminal repeats (LTR), which are 300 to 400 basepairs long.

tblastn - A BLAST program that compares a protein query sequence against a nucleotide sequence dataset dynamically translated in all six reading frames (both strands). The user must enter a AMINO ACID sequence and select one of the NUCLEOTIDE datasets (i.e., genoSc or GenBank) for the search.

tblastx - A BLAST program that compares the six-frame translations of a nucleotide sequence to the six-frame translations of a nucleotide sequence dataset. The user must enter a NUCLEOTIDE sequence and select one of the NUCLEOTIDE datasets (i.e., genoSc or GenBank) for the search.

Transmembrane Domain - Refers to the domains in amphipathic membrane proteins where the hydrophobic regions traverse the lipid bilayers of the membranes, while the hydrophilic regions extend on either side of the membrane and interact with water.

Transposon - Any of the five classes (TY1 through Ty5) of mobile genetic elements in yeast that contain long terminal repeats flanking a central epsilon element that encodes two gene products, TyA (structural component) and TyB (reverse transcriptase). Ty elements are retrotransposons that move about the genome via an RNA intermediate.

Tree-View - Tree-View refers to the display of parent-child relationships of GO terms within an ontology.

Unipolar budding - The development of conidia at one end of the parent cell.

Uniseriate - Having phialides that arise directly from the vesicle in species of Aspergillus.

Verrucose - Having warts.

Verticil - A whorl of conidiogenous cells or conidiophores arising from a common point.

Verticillate - Having verticils.

Vesicle - A swollen cell; the swollen apices of some conidiophores or sporangiophores.

Villose - Bearing long, hair-like appendages.

Variable numbers of tandem repeats (VNTRs) - DNA sequence blocks of 2-60 base pairs which are repeated from two to more than 20 times in different individuals. This polymorphism makes VNTRs very useful DNA markers used in genomic mapping, linkage analysis and also DNA fingerprinting.

Vector - Any agent that transfers material (typically DNA) from one host to another. Typically DNA vectors are autonomous DNA elements (such as plasmids) that can be manipulated and integrated into a hostís DNA or recombinant viruses.

Weight matrix - The density of binding sites in a gene or sequence can be used to derive a ratio of density for each element in a pattern of interest. The combined individual density ratios of all elements are then collectively used to build a scoring profile known as a weight matrix. This profile can be used to test the prediction of the identification of the selected pattern and the ability of the algorithm to discriminate them from non-pattern sequences.

Western blot - Technique in which specific antibodies are used to identify their antigens from a mixture of proteins. Typically, these proteins mixtures are first separated by electrophoresis and then transfered onto nylon sheets by electrotransfer. Radiolabeled or enzyme-linked antibodies are incubated with the sheets and unbound antibodies washed away allowing the position of the bound antibody to be revealed by autoradiography or color which is formed upon addition of a substrate.

Wild type - Form of a gene or allele that is considered the "standard" or most common.

Yeast GenBank - A collection of all GenBank sequences that were derived from Saccharomyces cerevisiae.

Yeast Swiss-Prot - The collection of Swiss-Prot protein sequences that are derived from Saccharomyces cerevisiae.

YPD - The Yeast Proteome Database maintained by BIOBASE. YPD contains physical, functional and some genetic information about Saccharomyces cerevisiae. YPD was originally developed and maintained by Proteome Inc. Access now requires a paid subscription.

Yeast - A unicellular budding fungus that reproduces by sexual, asexual, or both means. Pertaining to a unicellular budding fungus that reproduces by asexual means only.

Zonate - Having concentric bands of color or growth.

Zygospore - A resting spore in which meiosis will occur. Zygospores result from the fusion of two similar hyphal elements. They are characteristic of the Zygomycetes.

Zymogen - Some proteins are synthesized as zymogens, which are enzymatically inactive precursors of proteolytic enzymes. Zymogens usually become activated by posttranslational modifications, such as cleavage in a particular peptide sequence.

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