Difference between revisions of "FASTA"

From UFRC
Jump to navigation Jump to search
m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
 
(12 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__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:app|fasta}}
 
|{{#vardefine:url|http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml}}
 
|{{#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:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#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-->
Line 39: Line 24:
 
FASTA can be used to infer functional and evolutionary relationships between
 
FASTA can be used to infer functional and evolutionary relationships between
 
sequences as well as help identify members of gene families.
 
sequences as well as help identify members of gene families.
 
+
<!--Modules-->
==Available versions==
+
==Environment Modules==
* 34.26.5
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
<!-- -->
+
==System Variables==
{{#if: {{#var: mod}}|==Execution Environment and Modules==
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
 
* HPC_FASTA_BIN - executable directory
 
* HPC_FASTA_BIN - executable directory
 
 
==Available documentation==
 
==Available documentation==
 
Several man pages are available:
 
Several man pages are available:
 
* fasta3, fastf3, fasts3, map_db, prss3, pvcomp
 
* fasta3, fastf3, fasts3, map_db, prss3, pvcomp
 
Type "man MANPAGE" to access them at the command line.
 
Type "man MANPAGE" to access them at the command line.
 
 
{{#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.|}}
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} 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)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 18:54, 12 August 2022

Description

fasta website  

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.