Difference between revisions of "BLAST"

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== Installed version ==
== Installed version ==


The currently installed version is 2.2.26 and version 2.6.0.
These versions are installed and and currently available...


== Using BLAST with the HPC Cluster ==
... on envirnoment ''hpc-uniol-env'':
*'''BLAST/2.2.26'''
*'''BLAST/2.6.0'''
*'''BLAST+/2.7.1'''-intel-2016b-Python-2.7.12
 
... on environment ''hpc-env/6.4'':
*'''BLAST+/2.7.1'''-intel-2018a
*'''BLAST+/2.7.1'''-foss-2017b-Python-2.7.14
 
 
... on environment ''hpc-env/8.3'':
*'''BLAST/2.11.0'''-Linux_x86_64
*'''BLAST+/2.11.0'''-gompi-2019b
*'''BLAST+/2.13.0'''-gompi-2019b
 
== Available Commands ==
 
BLAST offers three categories of applications:
 
* '''search tools''': blastn, blastp, blastx, tblastx, tblastn, psiblast, rpsblast, rpstblastn
* '''BLAST database tools''': makeblastdb, blastdb_aliastool, makeprofiledb, blastdbcmd
* '''sequence filtering tools''': segmasker, dustmasker, windowmasker
 
== Using BLAST ==


If you want to find out more about BLAST on the HPC Cluster, you can use the command
If you want to find out more about BLAST on the HPC Cluster, you can use the command
Line 15: Line 39:
This will show you basic informations e.g. a short description and the currently installed version.
This will show you basic informations e.g. a short description and the currently installed version.


To load the desired module, use the command, e.g.
To load the desired version of the module, use the command, e.g.


  module load BLAST/2.6.0-Linux_x86_64  
  module load BLAST/2.6.0-Linux_x86_64  


Always remember: this command is case sensitive!
Always remember: this command is case sensitive!
 
<!--
BLAST offers three categories of applications:
== Using BLAST with the HPC Cluster ==
 
-->
* '''search tools''': blastn, blastp, blastx, tblastx, tblastn, psiblast, rpsblast, rpstblastn
* '''BLAST database tools''': makeblastdb, blastdb_aliastool, makeprofiledb, blastdbcmd
* '''sequence filtering tools''': segmasker, dustmasker, windowmasker


== Documentation ==
== Documentation ==

Latest revision as of 17:14, 22 March 2022

Introduction

In bioinformatics, BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.

Installed version

These versions are installed and and currently available...

... on envirnoment hpc-uniol-env:

  • BLAST/2.2.26
  • BLAST/2.6.0
  • BLAST+/2.7.1-intel-2016b-Python-2.7.12


... on environment hpc-env/6.4:

  • BLAST+/2.7.1-intel-2018a
  • BLAST+/2.7.1-foss-2017b-Python-2.7.14


... on environment hpc-env/8.3:

  • BLAST/2.11.0-Linux_x86_64
  • BLAST+/2.11.0-gompi-2019b
  • BLAST+/2.13.0-gompi-2019b

Available Commands

BLAST offers three categories of applications:

  • search tools: blastn, blastp, blastx, tblastx, tblastn, psiblast, rpsblast, rpstblastn
  • BLAST database tools: makeblastdb, blastdb_aliastool, makeprofiledb, blastdbcmd
  • sequence filtering tools: segmasker, dustmasker, windowmasker

Using BLAST

If you want to find out more about BLAST on the HPC Cluster, you can use the command

module spider blast

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load BLAST/2.6.0-Linux_x86_64 

Always remember: this command is case sensitive!

Documentation

The full documentation can be found here.

Direct link to the command line manual (PDF viewer required): BLAST® Command Line Applications User Manual