A brief introduction to HMMSEARCH
The program HMMSEARCH, belonging to the HMMER package, compares a query profile HMM against a sequence library. It generates a list of significantly similar sequence matches. This tool is very useful for homology detection, for the detection of motifs in protein sequences...
For further details, see HMMER homepage.

Availability in NPS@
HMMSEARCH is available :

The searching options correspond to the choice of the protein library and to the choice of E-value cut-off for complete sequences. By default, the cutoff for E-values per sequence is set to 10.0 (an E-value per sequence takes into account all matches found in the sequence) : all matches found in a sequence that passed the per-sequence threshold will be reported. You can also choose to use the forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores.

NPS@ HMMSEARCH output example
The NPS@ HMMSEARCH output is divided into four parts.