HMMER
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| Revision as of 18:48, 20 June 2007 (edit) Mauro (Talk | contribs) (New page: 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 fr...) ← Previous diff |
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| ===Available programs === | ===Available programs === | ||
| :HMMER available programs are: | :HMMER available programs are: | ||
| - | [http://bioinfo.ceinge.unina.it/tools/winterf/hmmalign.php hmmalign]''': Align multiple sequences to a profile HMM. | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/hmmalign.php hmmalign]''': Align multiple sequences to a profile HMM. |
| - | [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/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/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). |
| :The userguide of HMMER package is available [http://bioinfo.ceinge.unina.it/help/hmmer/ here] | :The userguide of HMMER package is available [http://bioinfo.ceinge.unina.it/help/hmmer/ here] | ||
Revision as of 18:50, 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.
- 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
