Motif/Pattern/Profile searches

This page has been developed for a review on motif and profile searches to appear in "Methods in Enzymology" 1995 (ed.R.F. Doolittle) by Peer Bork and Toby Gibson. It is not comprehensive and some of the pointers might be out of date if you touch this page. We are grateful for pointers to other motif/pattern profile searches for protein sequences.

Searchable motif and pattern databases

Geneva's Expasy - PROSITE , motif search ICR, Kyoto, or scan of profiles at ISREC
BLOCKS home page at Hutchinson, Seattle
PRINTS home page at UC London
PIMA pattern DB and other search facilities at BCM (Houston)
one PRODOM page at Toulouse

Motif and profile searches

regular expression search at Univ.Wash.
parallelized PROFILESEARCH at the Weizmann inst.
PATSCAN searches for motifs at Argonne
PatternFind allows database searches with pattern or profile-based PROSITE descriptions
PROFILE method description [Document only!]
Pmotif finds protein motifs in DNA
HMMER HMM descriptions and converter to profile at St. Louis

WWW and FTP servers for single sequence exhaustive database searches

Blast at NCBI or at Stanford U. or SRS-linked or at ISREC (incl) EPFL Blast (distributed memory)
Blitz at EBI
FASTA at crihan in france or at EBI

Some programs that can be obtained from the following ftp adresses:

ftp addresses for motif and profile search programs

Barton's flexible patterns:ftp://geoff.biop.ox.ac.uk, more infos
Propat: ftp.mdc-berlin.de/pub/makpat [property pattern search]
SOM: ftp.mdc-berlin.de/pub/neural [pattern extraction/ search using hierarchical neural networks]
Searchwise:ftp SABLE.OX.AC.UK/pub/users [improved profile (incl. DNA database) searches]
PROFILE:ftp.ebi.ac.uk/pub/software/unix/ [classical profilesearch]
TPROFILESEARCH: ftp.ebi.ac.uk/pub/software/vax/egcg[improfed profile search that allows 6-frame DNA database translations]
CAP:ftp://ncbi.nlm.nih.gov/pub/koonin/cap [blastp output parser]

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Peer Bork

Last update: June 29, 1995