HMMER
From Wiki CEINGE
HMMER HMMER is a freely distributable implementation of profile HMM software for sequence analysis.
How to reach and use HMMER
- HMMER applications can be searched and launched from the Bioinfo website through the PROGsDB.
- Most of HMMER applications can be directly launched by CAPRI.
- In the VLS environment, the HMMER package is fully available for command line use in the directory /bioprogs/hmmer.
Available programs
- HMMER available programs are:
- hmmalign: Align multiple sequences to a profile HMM.
- hmmbuild: Build a profile HMM from a given multiple sequence alignment.
- hmmcalibrate: Determine appropriate statistical significance parameters for a profile HMM prior to doing database searches.
- hmmconvert: Convert HMMER profile HMMs to other formats, such as GCG profiles.
- hmmemit: Generate sequences probabilistically from a profile HMM.
- hmmfetch: Retrieve an HMM from an HMM database
- hmmindex: Create a binary SSI index for an HMM database
- hmmpfam: Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the query sequence).
- hmmsearch: Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled family).
- The userguide of HMMER package is available here
References
- Rice P, Longden I and Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends in Genetics, 2000, 16:276-277.
- For more details about HMMER, visit the HMMER web site