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PROSITE: - Dictionary
of protein sites and patterns. PROSITE is a method of determining
what is the function of uncharacterized proteins translated from genomic
or cDNA sequences. It consists of a database of biologically significant
sites, patterns and profiles that help to reliably identify to which known
family of protein (if any) a new sequence belongs. PROSITE references
and references on profiles
from PROSITE
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Pfam: Pfam
is a large collection of multiple sequence alignments and hidden Markov
models covering many common protein domains.Version 5.0 of Pfam (January
2000) contains alignments and models for 2008 protein families, based on
the Swissprot 38 and SP-TrEMBL 11 protein sequence databases.
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SMART; database of
protein domains (defined as HMM profiles) and protein families.
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InterPro:
Database of protein families defined by presence of common motifs and domains,
defined in several databases such as Pfam, SMART, Prosite, and other.
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BLOCKS: Blocks are
multiply aligned ungapped segments corresponding to the most highly conserved
regions of proteins. Block Searcher, Get Blocks and Block
Maker are aids to detection and verification of protein sequence homology.
They compare a protein or DNA sequence to a database of protein blocks,
retrieve blocks, and create new blocks, respectively.
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PRINTS:
PRINTS is a compendium of protein fingerprints. A fingerprint is
a group of conserved motifs used to characterise a protein family; its
diagnostic power is refined by iterative scanning of a
SWISS-PROT/TrEMBL
composite. Usually the motifs do not overlap, but are separated along a
sequence, though they may be contiguous in 3D-space. Fingerprints can encode
protein folds and functionalities more flexibly and powerfully than can
single motifs, full diagnostic potency deriving from the mutual context
provided by motif neighbours. References
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ProDom:
The
ProDom protein domain database consists of an automatic compilation of
homologous domains detected in the SWISS-PROT database by the DOMAINER
algorithm (Sonnhammer, E.L.L. & Kahn, D., 1994, Protein Sci. 3:482-492).
It has been devised to assist with the analysis of the domain arrangement
of protein. Last release of ProDom families was generated automatically
using PSI-BLAST with a profile built from the seed aligments of Pfam-A
3.4 families.
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GeneFIND (Gene
Family Identification Network Design) is an integrated database search
system that combines several search/alignment tools and ProClass database
to provide rapid and accurate gene family classification with enriched
family information. The objectives are to improve speed and sensitivity,
differentiate global and motif similarities, and provide collective information
in an integrated platform that alleviates human annotation effort. It was
used to identify several thousands of new ProSite members, which have been
incorporated into out ProClass_Motif sub-database
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