Difference between revisions of "NCBI BLAST+"

From UFRC
Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:biologyCategory:bioinformatics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|ncbi_blast}} |{{#vardefine:url|ftp://ftp.ncbi.nlm.nih.g...")
 
 
(One intermediate revision by one other user not shown)
Line 1: Line 1:
[[Category:Software]][[Category:biology]][[Category:bioinformatics]]
+
[[Category:Software]][[Category:biology]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|ncbi_blast}}
 
|{{#vardefine:app|ncbi_blast}}
Line 24: Line 24:
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documents directory
+
* HPC_{{uc:{{#var:app}}}}_DOC - documents directory
 
* BLASTDB - BLAST database location
 
* BLASTDB - BLAST database location
 
<!--Configuration-->
 
<!--Configuration-->

Latest revision as of 19:55, 12 August 2022

Description

ncbi_blast website  

The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s.

Environment Modules

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

System Variables

  • HPC_NCBI_BLAST_DIR - installation directory
  • HPC_NCBI_BLAST_BIN - executable directory
  • HPC_NCBI_BLAST_DOC - documents directory
  • BLASTDB - BLAST database location