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Words
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Description
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| Pattern
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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. |
| Profile
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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. |
| Protein families
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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. |
| P value
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The probability of an alignment occurring with the score in question or better. |
| Pairwise alignment
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In a pairwise alignment, two sequences are padded by gaps, to achieve same length, and to display maximum similarity/conservation on a character-by-character basis. |
| Paralogous
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Homologous sequences (sequences that share a common evolutionary ancestor) that diverged by gene duplication, as opposed to orthologs, which diverged by speciation. |
| Perl
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An interpreted computer language for easily manipulating text, files and processes. |
| Phylogeny
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A classification scheme that indicates the evolutionary relationships between organisms. |
| PROSITE
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A database of "patterns" (regular expressions) specific for various protein motifs |
