Difference between revisions of "FASTA"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "")
 
(7 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]]
 
+
{|<!--Main settings - REQUIRED-->
{|
 
<!--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" -->
 
 
 
|{{#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 30: 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-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
[[Modules|modules documentation]]
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
+
==System Variables==
*{{#var:app}}
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* 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.|}}

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.