HMMER
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| HMMER is a freely distributable implementation of profile HMM software for sequence analysis. | HMMER is a freely distributable implementation of profile HMM software for sequence analysis. | ||
| - | === How to reach and use HMMER === | + | ===How to reach and use HMMER=== |
| :HMMER applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]]. | :HMMER applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]]. | ||
| :Most of HMMER applications can be directly launched by [[CAPRI]]. | :Most of HMMER applications can be directly launched by [[CAPRI]]. | ||
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| :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmbuild.php hmmbuild]''': Build a profile HMM from a given multiple sequence alignment. | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmbuild.php hmmbuild]''': Build a profile HMM from a given multiple sequence alignment. | ||
| :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmcalibrate.php hmmcalibrate]''': Determine appropriate statistical significance parameters for a profile HMM prior to doing database searches. | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmcalibrate.php hmmcalibrate]''': Determine appropriate statistical significance parameters for a profile HMM prior to doing database searches. | ||
| - | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmconvert.php hmmconvert]''': Convert HMMER profile HMMs to other formats, such as GCG profiles. | ||
| :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmemit.php hmmemit]''': Generate sequences probabilistically from a profile HMM. | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmemit.php hmmemit]''': Generate sequences probabilistically from a profile HMM. | ||
| :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmfetch.php hmmfetch]''': Retrieve an HMM from an HMM database | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmfetch.php hmmfetch]''': Retrieve an HMM from an HMM database | ||
| - | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmindex.php hmmindex]''': Create a binary SSI index for an HMM database | ||
| :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmpfam.php hmmpfam]''': Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the query sequence). | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmpfam.php hmmpfam]''': Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the query sequence). | ||
| :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmsearch.php hmmsearch]''': Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled family). | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmsearch.php hmmsearch]''': Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled family). | ||
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| === References === | === References === | ||
| - | + | :For more details about HMMER package, visit the [http://hmmer.janelia.org/ HMMER web site] | |
| - | :For more details about HMMER, visit the [http://hmmer.janelia.org/ HMMER web site] | + | |
Revision as of 18:52, 20 June 2007
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.
- hmmemit: Generate sequences probabilistically from a profile HMM.
- hmmfetch: Retrieve an HMM from 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
- For more details about HMMER package, visit the HMMER web site
