Pfam - Pfam is a large
collection of multiple sequence alignments and hidden Markov
models covering many common protein families. Pfam version 16.0
(November 2004) contains alignments and models for 7677 protein
families, based on the Swissprot 44.5 and SP-TrEMBL 27.5 protein
- at the Fred Hutchinson Cancer Research Center Blocks WWW
server. Search your protein or DNA sequence against a Blocks
eBLOCKS - database
of protein sequence blocks -- ungapped alignments of highly
conserved regions among a protein family or superfamily.
eMOTIF - collection
of more than 170000 highly specific and sensitive protein sequence
motifs representing conserved biochemical properties and biological
The ScanProsite tool allows to scan protein sequence(s) (either
from Swiss-Prot or TrEMBL or provided by the user) for the occurrence
of patterns, profiles and rules (motifs) stored in the PROSITE
database, or to search protein database(s) for hits by specific
motif(s). The program PRATT can be used to generate your own
- The Protein Domain Database. Is a comprehensive set of protein
domain families automatically generated from the SWISS-PROT
and TrEMBL sequence databases.
- PatScan is a pattern matcher which searches protein or nucleotide
(DNA, RNA, tRNA etc.) sequence archives for instances of a pattern
which you input.