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BLAST

 

From the HT-BLAST Homepage:

BLAST (Basic Local Alignment Search Tool) is a collection of searching programs for biological sequence databases. The program uses the BLAST algorithm (see references below), to compare protein or DNA sequence queries to protein or DNA sequence databases.

Invoking

HT-BLAST is part of the htblast module. This module is not loaded by default, so it is necessary to use the module load command to load it prior to invoking HT-BLAST.

Multiple versions of HT-BLAST are are available under modules: The htblast/2.0.11_32 modulefile loads the 32-bit version of HT-BLAST 2.0.11. The htblast/2.0.11_64 modulefile loads the 64-bit version of HT-BLAST. The default is htblast/2.0.11_32.

  • Typing module load htblast at a command prompt will make the HT-BLAST commands available.
  • The formatdb command can be used to convert your database from FASTA ascii format to BLAST binary format
  • The blockhead command can be used run blast. The NUM_THREADS enviroment variable controls the number of CPUs that blockheadwill use (by default it is set to 1).
Getting Help

Help is available at the following locations:

Useful Resource

NCBI BLAST hompage.

Installation

HT-BLAST is available from Notre Dame AFS space in the htblast module. This module must be loaded by the user.