HMMER
From Wiki CEINGE
(Difference between revisions)
| Revision as of 18:50, 20 June 2007 (edit) Mauro (Talk | contribs) ← Previous diff |
Current revision (19:04, 20 June 2007) (edit) (undo) Mauro (Talk | contribs) |
||
| (3 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| HMMER | HMMER | ||
| - | HMMER | + | Profile hidden Markov models (HMMs) are used for searching databases using a statistical description of a sequence family's consensus. |
| + | HMMER (version 2.3.2), a freely implementation of HMM software for sequence analysis is installed and runs on the [[cluster]] server. It is highly connected both with the Bioinformatic service and research group activity. For example, it has been used for the automatic identification of SLSs families in bacterial genomes, described in the [[Bacterial_RNAs]] section. HMMER programs are computational expansive, but the ability to run them on the cluster server allows to reduce their time execution, expecially in case of analysis of large amount of data. | ||
| - | === 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]]. | ||
| Line 12: | Line 13: | ||
| :*'''[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). | ||
| Line 23: | Line 22: | ||
| === 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] | + | |
Current revision
HMMER Profile hidden Markov models (HMMs) are used for searching databases using a statistical description of a sequence family's consensus. HMMER (version 2.3.2), a freely implementation of HMM software for sequence analysis is installed and runs on the cluster server. It is highly connected both with the Bioinformatic service and research group activity. For example, it has been used for the automatic identification of SLSs families in bacterial genomes, described in the Bacterial_RNAs section. HMMER programs are computational expansive, but the ability to run them on the cluster server allows to reduce their time execution, expecially in case of analysis of large amount of data.
[edit] 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.
[edit] 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
[edit] References
- For more details about HMMER package, visit the HMMER web site
