ScanProsite: a reference implementation of a PROSITE scanning tool.
نویسندگان
چکیده
Many different software tools are available publicly to scan the PROSITE database of protein families. However, none of them, to our knowledge, wholly implements the PROSITE syntax, or satisfies all the rules for scanning a pattern against a sequence. We hereby propose a strict definition of how a PROSITE pattern is to be scanned against a sequence, and provide a reference implementation of a tool to scan PROSITE patterns, rules and profiles against protein sequences.
منابع مشابه
PPMuSA: PROSITE-Pattern Matcher Using Suffix Array
PPMuSA is a pattern matching program for PROSITE [2] signature patterns against amino acid sequence database. To characterize a group of protein among others, it is important work to find occurrences of a signature in an amino acid sequence of the protein. Such signatures are compiled in databases. The PROSITE is one of the databases of signatures that distinguish members of a protein families ...
متن کاملScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
ScanProsite--http://www.expasy.org/tools/scanprosite/--is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules--context-dependent annotation templates--to detect functional and structural intra-domain residues. The detection of those features enhances the power of funct...
متن کاملThe PROSITE database
The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to a documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE database is now complemented by a series of rules that can give more precise informat...
متن کاملProRule: a new database containing functional and structural information on PROSITE profiles
MOTIVATION Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins. SUMMARY We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or function...
متن کاملPROSITE, a protein domain database for functional characterization and annotation
PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally cr...
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ورودعنوان ژورنال:
- Applied bioinformatics
دوره 1 2 شماره
صفحات -
تاریخ انتشار 2002