[WashU] HMMER
User's Guide


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Subsections

hmmsearch - search a sequence database with a profile HMM

Synopsis

hmmsearch [options] hmmfile seqfile

Description

hmmsearch reads an HMM from hmmfile and searches seqfile for significantly similar sequence matches.

seqfile will be looked for first in the current working directory, then in a directory named by the environment variable BLASTDB. This lets users use existing BLAST databases, if BLAST has been configured for the site.

hmmsearch may take minutes or even hours to run, depending on the size of the sequence database. It is a good idea to redirect the output to a file.

The output consists of four sections: a ranked list of the best scoring sequences, a ranked list of the best scoring domains, alignments for all the best scoring domains, and a histogram of the scores. A sequence score may be higher than a domain score for the same sequence if there is more than one domain in the sequence; the sequence score takes into account all the domains. All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and bit score thresholds may also be applied to the domain list using the -domE and -domT options.

Options

Expert Options


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Next: alistat - show statistics Up: Manual pages Previous: hmmpfam - search a


Direct comments and questions to <eddy@genetics.wustl.edu>