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

A brief introduction to HMMBUILD
The program HMMBUILD, belonging to the HMMER package, generates a profile HMM (hidden Markov models) from a multiple sequence alignment. Profile HMMs are statistical models of the primary structure consensus of a sequence family. A profile HMM can typically be used in homology detection by comparing a query profile HMM against a DNA or protein sequence library.
For further details, see the HMMER homepage.

Availability in NPS@
HMMBUILD is available :

• from a dedicated HMMBUILD page (starting with multiple protein sequence alignment in Clustal W format)
• from multiple sequence alignment output computed by means of KALIGN, MAFFT and MUSCLE

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

NPS@ HMMBUILD output
The HMMBUILD profile allows you to continue your analysis with a search against a protein sequence database thanks to HMMSEARCH.

References

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