Overview

Overview of APPLICATION

  1. the science
    • BLAST: Basic Local Alignment Search Tool. DNA sequence matcher.
  2. citations
  3. official web page blast.ncbi.nlm.nih.gov/Blast.cgi

 

Running the APPLICATION
  1. How to run APPLICATION (main module to load, required parameters)
    • module load yorkmodule unload openmpi module unload intel;module load gnu/4.7.1module load blast (ormodule load blast/2.2.27+ for a specific version)
  2. Example script to run (if not obvious)
    • blast comprises a number of executables. Executables are:
    • blastdb_aliastool
    • dustmasker
    • segmasker
    • blastdbcheck
    • gene_info_reader
    • seqdb_demo
    • blastdbcmd
    • legacy_blast.pl
    • seqdb_perf
    • blastdbcp
    • makeblastdb
    • setup.sh
    • blast_formatter
    • makembindex
    • tblastn
    • blastn
    • makeprofiledb
    • tblastx
    • blastp
    • project_tree_builder
    • update_blastdb.pl
    • blastx
    • psiblast
    • windowmasker
    • convert2blastmask
    • rpsblast
    • windowmasker_2.2.22_adapter.py
    • datatool
    • rpstblastn
    • deltablast
    • seedtopNormally a user will use a preformatted database (Seewww.ncbi.nlm.nih.gov/mapview) and run one of the commands starting blast on it (blastn,blastxblastp). As of 26/11/12 the default format fordatabases changed to ‘nt’.For further documentation see: blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs
  3. Ideally, an example dataset and scaling results will be presented in order to give users an idea of the number of cores and memory usage for the software.
    • To be added.

 

Licensing and Systems that have APPLICATION
  1. licence info with link (or text indicating the file on disk) containing the full licensewww.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE
                                   PUBLIC DOMAIN NOTICE                  National Center for Biotechnology Information     This software/database is a "United States Government Work" under the     terms of the United States Copyright Act.  It was written as part of     the author's official duties as a United States Government employee and     thus cannot be copyrighted.  This software/database is freely available     to the public for use. The National Library of Medicine and the U.S.     Government have not placed any restriction on its use or reproduction.     Although all reasonable efforts have been taken to ensure the accuracy     and reliability of the software and data, the NLM and the U.S.     Government do not and cannot warrant the performance or results that     may be obtained by using this software or data. The NLM and the U.S.     Government disclaim all warranties, express or implied, including     warranties of performance, merchantability or fitness for any particular     purpose.     Please cite the author in any work or product based on this material.
  2. versions available
    • 2.2.27+
  3. Other (tier3) places to run application
    • White Rose Grid, York.

 

Further Information
  1. First point of contact should be the York help desk.
  2. Any notable build details
    • Requires gnu/4.7.1 module to compile. This is incompatible with the intel (and thus the openmpi) modules.
    • There is a mpiblast project but it seems to be moribund and so the incompatibility with openmpi is not likely to be a serious issue.
  3. Any notable details in using it with the module environment
    • Requires gnu/4.7.1 so module unload openmpi and module unload intel.
  4. Any notable details in using it e.g. command to launch it as a parallel program, special batch queue details
    • None.
  5. Troubleshooting
    1. NULL pointer issues when running blastp
      • A user reported NULL pointer issues. This seems to be related to corrupt formatted databases but the same database does work with older versions of blast, so blast-2.2.7+ is more picky about this. The solution is to grab a clean copy of the formatted database, or regenerate the data from an unformatted version using the blast database manipulation tools.