Difference between revisions of "HMMER"
Moskalenko (talk | contribs) m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "") |
|||
| (9 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|hmmer}} | |{{#vardefine:app|hmmer}} | ||
|{{#vardefine:url|http://hmmer.janelia.org/}} | |{{#vardefine:url|http://hmmer.janelia.org/}} | ||
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | ||
| − | |||
| − | |||
| − | |||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| Line 33: | Line 27: | ||
strength came at significant computational expense, but in the new HMMER3 | strength came at significant computational expense, but in the new HMMER3 | ||
project, HMMER is now essentially as fast as BLAST. | project, HMMER is now essentially as fast as BLAST. | ||
| − | |||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_HMMER_BIN - executable directory | * HPC_HMMER_BIN - executable directory | ||
| − | {{#if: {{#var: exe}}|== | + | {{#if: {{#var: exe}}|==Additional Information== |
| − | + | phmmer and hmmsearch only work with fasta formatted target sequence databases. We provide the following fasta formatted databases either downloaded or extracted from the BLAST databases: | |
| + | * [http://www.uniprot.org/ UniProt] - /project/bio/fasta/uniprot/uniprot_sprot.fasta | ||
| + | * [http://www.ncbi.nlm.nih.gov/protein NCBI NR] - /project/bio/fasta/nr/nr.fa | ||
| + | * [http://www.ncbi.nlm.nih.gov/protein NCBI RefSeq] - /project/bio/fasta/refseq/refseq_protein.fa | ||
| + | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Latest revision as of 18:18, 15 August 2022
Description
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
Environment Modules
Run module spider hmmer to find out what environment modules are available for this application.
System Variables
- HPC_HMMER_DIR - installation directory
- HPC_HMMER_BIN - executable directory
Additional Information
phmmer and hmmsearch only work with fasta formatted target sequence databases. We provide the following fasta formatted databases either downloaded or extracted from the BLAST databases:
- UniProt - /project/bio/fasta/uniprot/uniprot_sprot.fasta
- NCBI NR - /project/bio/fasta/nr/nr.fa
- NCBI RefSeq - /project/bio/fasta/refseq/refseq_protein.fa