hmmsearch

hmmsearch Search a sequence database with a profile HMM.

hmmsearch [options] hmmfile seqfile

Options

-h

Print brief help; includes version number and summary of all options, including expert options.

-A n

Limits the alignment output to the n best scoring domains.

-E x

Set the E-value cutoff for the per-sequence ranked hit list to x, where x is a positive real number.

-T x

Set the bit score cutoff for the per-sequence ranked hit list to x, where x is a real number.

-Z n

Calculate the E-value scores as if we had seen a sequence database of n sequences.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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