Primary European nucleotide sequence resource for DNA and RNA sequences directly submitted
from individual researchers, genome sequencing projects and patent applications.
Integrated view of the commonly used secondary protein databases (PROSITE,
PRINTS, ProDom, Pfam), predicting functional sites and domains, unifying format
and nomenclature.
Kyoto Encyclopedia of Genes and Genomes (KEGG) is an effort to computerize current
knowledge of molecular and cellular biology in terms of the information pathways that
consist of interacting molecules or genes and to provide links from the gene catalogues
produced by genome sequencing projects.
The Protein Information Resource (PIR), in collaboration with MIPS and JIPID, produces
the PIR-International Protein Sequence Database (PIR-PSD), a comprehensive, non-redundant,
expertly annotated, fully classified and extensively cross-referenced protein sequence database.
Compendium of protein fingerprints (group of conserved motifs used to characterize a
protein family), using iterative scanning of a composite of Swiss-Prot + TrEMBL. 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, their full diagnostic potency deriving from the mutual
context afforded by motif neighbours.
Proteome, Inc. provides a variety of products and services to integrate the accumulated
knowledge from the research literature with genomic information and software tools. Databases
maintained at Proteome, Inc. include WormPD and YPD.
Database of protein families and domains. It consists of biologically significant sites,
patterns and profiles that help to reliably identify to which known protein family (if
any) a new sequence belongs.
SMART (a Simple Modular Architecture Research Tool) allows the identification and
annotation of genetically mobile domains and the analysis of domain architectures. More
than 500 domain families found in signalling, extracellular and chromatin-associated
proteins are detectable. These domains are extensively annotated with respect to phyletic
distributions, functional class, tertiary structures and functionally important residues.
Each domain found in a non-redundant protein database as well as search parameters and
taxonomic information are stored in a relational database system. User interfaces to
this database allow searches for proteins containing specific combinations of domains
in defined taxa.
Also known as SWALL. This is a comprehensive, non-redundant and up-to-date view of
the protein sequences currently publicly available. For a more detailed description of the
relationships between SPTR, Swiss-Prot and TrEMBL etc please see the description of
SPTR in
SRS and
this Swiss-Prot
description
A curated protein sequence database which strives to provide a high level of annotations
(such as the description of the function of a protein, its domains structure, post-translational
modifications, variants, etc.), a minimal level of redundancy and high level of integration
with other databases.
