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The 20 years of PROSITE.

Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, de Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJ - Nucleic Acids Res. (2007)

Bottom Line: PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them.In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods.Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match.

View Article: PubMed Central - PubMed

Affiliation: Swiss Institute of Bioinformatics (SIB), Centre Medical Universitaire, Structural Biology and Bioinformatics Department, University of Geneva, 1 rue Michel Servet, CH-1211 Geneva, Switzerland.

ABSTRACT
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 profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods. The latest version of PROSITE (release 20.19 of 11 September 2007) contains 1319 patterns, 745 profiles and 764 ProRules. Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match. PROSITE is available on the web at: http://www.expasy.org/prosite/.

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The web form and the output of the PROSITE ‘MyDomains’ image creator tool. A very simple syntax allows the user to define the shape, colour, size and name of one or several domains. Specific residues and ranges can also be marked.
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Figure 2: The web form and the output of the PROSITE ‘MyDomains’ image creator tool. A very simple syntax allows the user to define the shape, colour, size and name of one or several domains. Specific residues and ranges can also be marked.

Mentions: We have made available to PROSITE users our tool that generates domain images to represent protein architectures. For a given protein, the user can enter in a web form the size of the protein, the positions of the domains, their names and, for each domain, the colour and the shape of the wanted image. The web form returns an image in Portable Network Graphics (png) format that can be integrated into any publication (Figure 2). The tool is accessible at the following address: http://www.expasy.org/tools/mydomains/.Figure 2.


The 20 years of PROSITE.

Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, de Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJ - Nucleic Acids Res. (2007)

The web form and the output of the PROSITE ‘MyDomains’ image creator tool. A very simple syntax allows the user to define the shape, colour, size and name of one or several domains. Specific residues and ranges can also be marked.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238851&req=5

Figure 2: The web form and the output of the PROSITE ‘MyDomains’ image creator tool. A very simple syntax allows the user to define the shape, colour, size and name of one or several domains. Specific residues and ranges can also be marked.
Mentions: We have made available to PROSITE users our tool that generates domain images to represent protein architectures. For a given protein, the user can enter in a web form the size of the protein, the positions of the domains, their names and, for each domain, the colour and the shape of the wanted image. The web form returns an image in Portable Network Graphics (png) format that can be integrated into any publication (Figure 2). The tool is accessible at the following address: http://www.expasy.org/tools/mydomains/.Figure 2.

Bottom Line: PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them.In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods.Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match.

View Article: PubMed Central - PubMed

Affiliation: Swiss Institute of Bioinformatics (SIB), Centre Medical Universitaire, Structural Biology and Bioinformatics Department, University of Geneva, 1 rue Michel Servet, CH-1211 Geneva, Switzerland.

ABSTRACT
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 profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods. The latest version of PROSITE (release 20.19 of 11 September 2007) contains 1319 patterns, 745 profiles and 764 ProRules. Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match. PROSITE is available on the web at: http://www.expasy.org/prosite/.

Show MeSH
Related in: MedlinePlus