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PROSITE: A documented database using patterns and profiles as motif descriptors

C. J. A. Sigrist
2002 Briefings in Bioinformatics  
Acknowledgements PROSITE is supported by grant no. 3100-63879.00 from the Swiss National Science Foundation. The PROSITE database and programs to use it are available online or for download  ...  The motif descriptors used in PROSITE are either patterns or profiles, which are derived from multiple alignments of homologous sequences.  ...  There can be several reasons why a profile and its documentation are considered as preliminary and not integrated in PROSITE.  ... 
doi:10.1093/bib/3.3.265 pmid:12230035 fatcat:fe35ztnojrdhdn6it2bff3rhku

The 20 years of PROSITE

N. Hulo, A. Bairoch, V. Bulliard, L. Cerutti, B. A. Cuche, E. de Castro, C. Lachaize, P. S. Langendijk-Genevaux, C. J. A. Sigrist
2007 Nucleic Acids Research  
PROSITE activities are also supported by the Swiss Federal Government through the Federal Office of Education and Science.  ...  ACKNOWLEDGEMENTS We wish to thank Tania Lima for critical reading of the manuscript and Laurent Falquet for the design of the ProRule logo.  ...  Patterns are thus not adapted to identify less-conserved regions or whole domains. In 1994, Philipp Bucher introduced in PROSITE 'generalized profiles' as new motif descriptors (2) .  ... 
doi:10.1093/nar/gkm977 pmid:18003654 pmcid:PMC2238851 fatcat:yewekwlzobd75hmhakmtdkhlcq

Recent improvements to the PROSITE database

N. Hulo
2004 Nucleic Acids Research  
The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or pro®les.  ...  We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures.  ...  PROSITE is supported by grant no. 3100-63879.00 from the Swiss National Science Foundation.  ... 
doi:10.1093/nar/gkh044 pmid:14681377 pmcid:PMC308778 fatcat:htpeobpylzhx5gxtblgbh5stka

The PROSITE database, its status in 1997

A. Bairoch, P. Bucher, K. Hofmann
1997 Nucleic Acids Research  
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein  ...  (if any) a new sequence belongs, or which known domain(s) it contains.  ...  The profile structure (5,6) used in PROSITE is similar to but slightly more general than the one introduced by Gribskov and coworkers (7); additional parameters allow representation of other motif descriptors  ... 
doi:10.1093/nar/25.1.217 pmid:9016539 pmcid:PMC146371 fatcat:livraaj3ezazjacwmcp6vpl6sm

The PROSITE database, its status in 1999

K. Hofmann, P. Bucher, L. Falquet, A. Bairoch
1999 Nucleic Acids Research  
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of proteins  ...  (if any) a new sequence belongs or which known domain(s) it contains.  ...  To use the PROSITE patterns and profiles you can make use of the following software tools.  ... 
doi:10.1093/nar/27.1.215 pmid:9847184 pmcid:PMC148139 fatcat:5gsrgivtybgu7mregm3pyunbsm

New and continuing developments at PROSITE

Christian J. A. Sigrist, Edouard de Castro, Lorenzo Cerutti, Béatrice A. Cuche, Nicolas Hulo, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios
2012 Nucleic Acids Research  
PROSITE (http://prosite.expasy.org/) 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, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical  ...  ACKNOWLEDGEMENTS The authors thank Fre´de´ric Bastian for helpful discussions regarding gene expression library databases and for the selection of multi-species tissues that are used in ScanProsite.  ... 
doi:10.1093/nar/gks1067 pmid:23161676 pmcid:PMC3531220 fatcat:wpxzlrpscfhbloaba56dxrvj4q

The PROSITE database, its status in 1995

A Bairoch
1996 Nucleic Acids Research  
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of proteins  ...  (if any) a new sequence belongs or which known domain(s) it contains.  ...  To use the PROSITE patterns and profiles you can make use of the following software tools.  ... 
doi:10.1093/nar/24.1.189 pmid:8594577 pmcid:PMC145570 fatcat:oifmuhfjnjgndnq5v2pucjdzwq

Systematic and automated discovery of patterns in PROSITE families

Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano
2000 Proceedings of the fourth annual international conference on Computational molecular biology - RECOMB '00  
The complete analysis is sufficiently rapid, taking less than a day for all PROSITE families, to enable the use this methodology for routine curation of existing motif and profile databases.  ...  PROSITE is a method for protein classification which relies on a database of biologically significant sites and patterns in protein sequences.  ...  The latter is a comprehensive non-redundant database of blocks derived from several databases of sequence motifs and profiles.  ... 
doi:10.1145/332306.332360 dblp:conf/recomb/HartRSC00 fatcat:lrmnv3zpxjdfhezqaanl2gwwvq

PROSITE, a protein domain database for functional characterization and annotation

Christian J. A. Sigrist, Lorenzo Cerutti, Edouard de Castro, Petra S. Langendijk-Genevaux, Virginie Bulliard, Amos Bairoch, Nicolas Hulo
2009 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors thank Marco Pagni for helpful discussions and ideas and Andrea H. Auchincloss for critical reading of the manuscript.  ...  GENERALITIES The PROSITE database uses two kinds of signatures or descriptors to identify conserved regions, i.e. patterns and generalized profiles, both having their own strengths and weaknesses defining  ...  Since the latest NAR database issue paper (4), PROSITE has increased its number of signatures to 1559 documentation entries, 1308 patterns, 863 profiles and 869 ProRules.  ... 
doi:10.1093/nar/gkp885 pmid:19858104 pmcid:PMC2808866 fatcat:3dk25oo67zgoteiueycrcyoimm

mmsearch: a motif arrangement language and search program

T. Junier, M. Pagni, P. Bucher
2001 Bioinformatics  
This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases.  ...  The program does not by itself search for the constituent motifs, and is thus independent of how they are detected, which allows it to use motif match data of various origins.  ...  A Web interface to mmsearch is available on the Hits Web site (URL given in the Section Abstract) where it can be used with PROSITE and Pfam motifs in the SwissProt, TrEMBL, trGEN and trEST databases  ... 
doi:10.1093/bioinformatics/17.12.1234 pmid:11751236 fatcat:6m6ws7fdcjdchcxvhdkzayvklm

Novel developments with the PRINTS protein fingerprint database

T. K. Attwood, M. E. Beck, A. J. Bleasby, K. Degtyarenko, A. D. Michie, D. J. Parry-Smith
1997 Nucleic Acids Research  
The PRINTS database of protein family 'fingerprints' is a diagnostic resource that complements the PROSITE dictionary of sites and patterns.  ...  The current version, 13.0, encodes ∼3000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on.  ...  PRINTS is built and maintained at UCL with support from the Royal Society (T.K.A. is a Royal Society University Research Fellow). The project benefits from use of the BBSRC SEQNET facility.  ... 
doi:10.1093/nar/25.1.212 pmid:9016538 pmcid:PMC146411 fatcat:fsja3tjejnc4ll6pyctwub4qmy

Progress with the PRINTS protein fingerprint database

T. Attwood
1996 Nucleic Acids Research  
PRINTS thus provides a useful adjunct to the widely used PROSITE dictionary of patterns.  ...  PRINTS is a compendium of protein motif 'fingerprints' derived from the OWL composite sequence database.  ...  PRINTS is built and maintained at UCL with support from the Royal Society (TKA is a Royal Society University Research Fellow); it is compiled with assistance from a BBSRC Link grant in Leeds (MEB, KD).  ... 
doi:10.1093/nar/24.1.182 pmid:8594576 pmcid:PMC145564 fatcat:q5ydsotlavcozbrsmirvyskuhu

The role of pattern databases in sequence analysis

T. K. Attwood
2000 Briefings in Bioinformatics  
Which should we use? This review focuses on a particular type of database that is increasingly used in the task of routine sequence analysisthe so-called pattern database.  ...  The paper aims to provide an overview of the current status of pattern databases in common use, outlining the methods behind them and giving pointers on their diagnostic strengths and weaknesses.  ...  Acknowledgements The author is grateful to the Royal Society for a University Research Fellowship.  ... 
doi:10.1093/bib/1.1.45 pmid:11466973 fatcat:2juyjx3qjvegjfza3vrpsosvne

The PRINTS Database of Protein Fingerprints: A Novel Information Resource for Computational Molecular Biology

T. K. Attwood, H. Avison, M. E. Beck, M. Bewley, A. J. Bleasby, F. Brewster, P. Cooper, K. Degtyarenko, A. J. Geddes, D. R. Flower, M. P. Kelly, S. Lott (+6 others)
1997 Journal of chemical information and computer sciences  
Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership.  ...  PRINTS is a compendium of protein motif fingerprints derived from the OWL composite sequence database.  ...  ACKNOWLEDGMENT PRINTS is built and maintained at UCL with support from the Royal Society (T.K.A. is a Royal Society University Research Fellow).  ... 
doi:10.1021/ci960468e pmid:9177000 fatcat:grmdrgamczc5dhj3yekolsfieu

Structural conservation of a short, functional, peptide-sequence motif

Susan Fox-Erlich
2009 Frontiers in Bioscience  
Krishna Kaduvera and Mr. Jay Vyas for useful discussions. This research was funded in part by US National Institutes of Health grants EB001496 and GM079689.  ...  The Prosite motif descriptors take two forms: patterns and profiles (13) . A Prosite pattern is a regular expression defining all peptide sequences which are to be considered a match.  ...  The developers of Prosite view profiles and patterns as complementary approaches.  ... 
doi:10.2741/3299 pmid:19273121 pmcid:PMC2654600 fatcat:emjzwlsmazhntlmv4sl56vocv4
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