Difference between revisions of "FASTA"

Latest revision as of 18:54, 12 August 2022

Description

The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Environment Modules

Run module spider fasta to find out what environment modules are available for this application.

System Variables

HPC_FASTA_DIR - installation directory
HPC_FASTA_BIN - executable directory

Available documentation

Several man pages are available:

fasta3, fastf3, fasts3, map_db, prss3, pvcomp

Type "man MANPAGE" to access them at the command line.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+[[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|fasta}}
 |{{#vardefine:url|http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml}}
-<!--Compiler and MPI settings - OPTIONAL -->
-|{{#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|1}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 39: / Line 24: @@
 FASTA can be used to infer functional and evolutionary relationships between
 sequences as well as help identify members of gene families.
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_FASTA_BIN - executable directory
 ==Available documentation==
 Several man pages are available:
 * fasta3, fastf3, fasts3, map_db, prss3, pvcomp
 Type "man MANPAGE" to access them at the command line.
 {{#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==