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Search with a profile against protein sequence databases


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


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Profile hidden Markov models
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4. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids."
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