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April 30th, 2024: NPS@ updated (see NEWS).

A brief introduction to HMMSEARCH
The program HMMSEARCH, belonging to the HMMER package, compares a query profile HMM (hidden Markov models) 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 the HMMER homepage.

Availability in NPS@
HMMSEARCH is available :

• from a dedicated HMMSEARCH page (starting from a profile HMM)
• from HMMBUILD output

Parameters
The user can select among HMMSEARCH parameters to adjust profile search (see HMMER User's Guide):

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

• PART 1:
  
  • You have a form to select matches found by HMMSEARCH, before extracting them (PART 3 below), according to :
    • the domain independent an E-value lesser or equal to a value of your choice (default 0.01)
    • the positions (from-to) within the profile .
  
  


• PART 2:
  This part corresponds to the list of matches (domains) found by HMMSEARCH. Theses matches are sorted by order of independent E-value (E-value per domain).
  For each match, you can see :
  • the match number
  • a checkbox to select/unselect sequence for the EXTRCAT step
  • the NPSA link allows you to apply NPS@ methods on the corresponding sequence after it is extracted from the query database
  • the database link to retrieve the database entry
  • the sequence description
  • the independent E-value with a link to the pairwise alignment
  
  


• PART 3:
  You have :
  • an EXTRACT form to retrieve selected sequences from searched database (full-length) or HMMSEARCH profile-sequence alignments (partial), and perform further analyses
  • for partial extraction, you can specify a minimal residue number for the extracted sequences
  • a checkbox allows you to remove identical sequences in the created database
  
  


• PART 4:
  You have :
  • a link on the original HMMSEARCH result text file.
  • a link on the original HMMSEARCH multiple sequence alignment text file (from all included sequence and domains).
  • a HMMBUILD submit button to compute a new profile HMM from the above MSA of included sequences, and then iterate the search.
  
  

References

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