What is PROSITE?
PROSITE, a protein domain database for functional characterization and annotation. PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them.
What information can I find from a PROSITE signature?
Each PROSITE signature is linked to an annotation document where the user can find information on the protein family or domain detected by the signature: origin of its name, taxonomic occurrence, domain architecture, function, 3D structure, main characteristics of the sequence, domain size and some references.
Is there a database for PROSITE profiles?
Sigrist C.J.A., De Castro E., Langendijk-Genevaux P.S., Le Saux V., Bairoch A., Hulo N. ProRule: a new database containing functional and structural information on PROSITE profiles. Bioinformatics. 2005;21:4060–4066.
What is the difference between motifs and profiles in PROSITE?
The motif descriptors used in PROSITE are either patterns or profiles, which are derived from multiple alignments of homologous sequences. PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns.
Is PROSITE a secondary database?
PROSITE and PRINTS are the only manually annotated secondary databases. The print is a diagnostic collection of protein fingerprints.
Who created PROSITE?
Amos BairochPROSITE, initially a 'signature' or pattern database, was created in 1988 by Amos Bairoch. It was first distributed through PC/Gene, the sequence analysis software suite he was developing at the time. The first release of PROSITE was made available in PC/Gene in March 1988 and contained 58 patterns.
What are PROSITE patterns?
PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns. Profiles and patterns have complementary qualities.
What is scan PROSITE?
ScanProsite allows to scan proteins for matches against the PROSITE collection of motifs as well as against user-defined patterns. At the beginning the user has to choose between three options: Option 1 - Submit PROTEIN sequences to scan them against the PROSITE collection of motifs.
What is the difference between Cath and SCOP?
These domains are classified in a hierarchical manner: SCOP sorts protein domains into classes, folds, superfamilies and families while the four major levels of CATH are class, architecture, topology and homologous superfamily.
What is Swiss-Prot database?
SWISS-PROT (1) is an annotated protein sequence database, which was created at the Department of Medical Biochemistry of the University of Geneva and has been a collaborative effort of the Department and the European Molecular Biology Laboratory (EMBL), since 1987.
How do you use PROSITE?
1:152:34DNASTAR - Finding PROSITE Patterns - YouTubeYouTubeStart of suggested clipEnd of suggested clipFirst select the pattern. And then select sites and features show pattern description at any timeMoreFirst select the pattern. And then select sites and features show pattern description at any time you can also view and search the pro site database. Simply by selecting sites.
How do you reference a PROSITE?
If you want to refer to the PROSITE methodology please cite: Sigrist C.J.A., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform.
What are Bioinformatics blocks?
Blocks are ungapped multiple alignments of related protein sequence segments that correspond to the most conserved regions of the proteins. The Blocks Database is a collection of blocks representing known protein families that can be used to compare a protein or DNA sequence with documented families of proteins.
What are bioinformatics prints?
PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures.
What is TrEMBL?
Introduction TrEMBL is a computer-annotated protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT.
What are motifs in biochemistry?
A motif is a short conserved sequence pattern associated with distinct functions of a protein or DNA. It is often associated with a distinct structural site performing a particular function. A typical motif, such as a Zn-finger motif, is ten to twenty amino acids long.
What is a protete?
PROSITE is an annotated collection of motif descriptors dedicated to the identification of protein families and domains. The motif descriptors used in PROSITE are either patterns or profiles, which are derived from multiple alignments of homologous sequences. PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns. Profiles and patterns have complementary qualities. Patterns, confined to small regions with high sequence similarity, are often powerful predictors of protein functions such as enzymatic activities. Profiles covering complete domains are more suitable for predicting protein structural properties.
Is Entrez the be all and end all source of protein sequence information?
Although Entrez might appear to be the be-all and end-all source of protein and nucleotide sequence information, this is not quite true. There are many smaller but well curated databases of biologic information that are not included among the databases that Entrez serves. These include the Prosite and Blocks databases of protein structural motifs, transcription factor databases, species-specific databases, and databases devoted to certain pathogens.
What is a protein?
PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor.
What is a protein signature?
Similarly, a protein signature can be used to assign a newly sequenced protein to a specific family of proteins and thus to formulate hypotheses about its function. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains.
How ProSite can support you
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Reference Case: Chemical Support Systems (CSS) Ltd
Chemical Support Systems (CSS) Ltd., a long-established chemical dosing equipment manufacturer based in Winsford, UK, was able to reduce its’ overall production time and cost by using a logistics platform for inventory challenges. With ProSite by GF Piping Systems the company now benefits from complete visibility of all the stock.
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