Difference between revisions of "HMMER"

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

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Homology]]
+[[Category:Software]][[Category:Biology]][[Category:Genomics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|hmmer}}
 |{{#vardefine:url|http://hmmer.janelia.org/}}
-<!--Compiler and MPI settings - OPTIONAL -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
-|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 31: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 HMMER is used for searching sequence databases for homologs of protein
 sequences, and for making protein sequence alignments. It implements methods
@@ Line 41: / Line 27: @@
 strength came at significant computational expense, but in the new HMMER3
 project, HMMER is now essentially as fast as BLAST.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-==Available versions==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 3.0
+==System Variables==
-<!-- -->
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-{{#if: {{#var: mod}}|==Running the application using modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 * HPC_HMMER_BIN - executable directory
-{{#if: {{#var: exe}}|==How To Run==
+{{#if: {{#var: exe}}|==Additional Information==
-WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+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==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==