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Search with a profile against protein sequence databases

OVERVIEW

Given a profile, protein sequence databases on GenomeNet service are retrieved to find out the protein families that have the same motif. The profile, either in PROSITE or Hmmer-Pfam format, could be calculated from the multiple sequence alignment or retrieved from motif library in DBGET service. (Look for PROSITE and Pfam library, respectively). The Pfsearch [1, 2] program, one of the Profile-related software tools package (Pftool) is used to retrieve with PROSITE format profile and Hmmsearch [3, 4], one of the HMMER package is used for Pfam format one, respectively. Target sequence libraries are

Reference

1. Gribskov, M., McLachlan, A.D., Eisenberg,D.
Profile analysis: detection of distantly related proteins.
Proc. Natl. Acad. Sci. USA 84:4355-4358 (1987)
PubMed: 87260806
2. Luethy R., Xenarios I., Bucher P.
Improving the sensitivity of the sequence profile method.
Prot. Sci. 3:139- 146 (1994)
PubMed: 7511453
3. Eddy S.R.
Profile hidden Markov models
Bioinformatics 14:755-763 (1998)
PubMed: 9918945
4. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids."
Durbin R., Eddy S., Krogh A., Mitchison G., Cambridge University Press (1998) 350 pages.