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.