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hmmer (version 1.0.0)

Query:

Sequences:

[--acc] Prefer accessions over names in output:

[--noali] Omit the alignment section from the main output:

This can greatly reduce the output volume

[--incE] Use an E-value of <= this value as the per-target inclusion threshold:

The default is 0.01, meaning that on average, about 1 false positive would be expected in every 100 searches with different query subsequences.

[--incdomE] Use a conditional E-value of <= this value as the per-domain inclusion threshold, in targets that have already satisfied the overall per-target inclusion threshold:

Note. Hidden Markov Model (HMM) searches take a substantial amount of time. For large input datasets it is advisable to allow overnight processing.

What it does

hmmscan is used to search sequences against collections of profiles. For each sequence in seqfile, use that query sequence to search the target database of profiles in hmmdb, and output ranked lists of the profiles with the most significant matches to the sequence.

hmmsearch is used to search one or more profiles against a sequence database. For each profile in "hmmfile", use that query profile to search the target database of profiles in "seqdb", and output ranked lists of the sequences with the most significant matches to the profile.

If using a user-supplied profile database, it needs to be pressed using hmmpress before it can be searched with hmmscan.

Author

Sean Eddy, Howard Hughes Medical Institute and Dept. of Genetics, Washington University School of Medicine

http://www.genetics.wustl.edu/eddy/

Manual

ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf