(NCBI) Blast

License

Non-commercial software, freely available to the public.

Users of this application should credit the code authors and the NGS accordingly and where applicable the specific site where the code is installed, when publishing work using NGS resources.

Running the Application on the NGS (General)

The input file, aadnafra.fsa, used in these examples can be found at:
gsiftp://ngs.rl.ac.uk:2811/apps/blast_ncbi/examples/aadnafra.fsa

In these examples the database (-d) we are searching is est_hum . This is stored in ${DB_PATH}/EBI_NUCLEOTIDE_DB/blast_DB directory in BLAST format. It is part of the EBI_NUCLEOTIDE database. $BLASTDB is already set to this path.

• Submission Using the UI/WMS

  To submit a Blast job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a blast.jdl

  Type = "Job";
  JobType = "Normal";
  Executable = "/usr/ngs/BLAST-NCBI";
  Arguments = "blastall -p blastn -d est_hum -i aadnafra.fsa -a 1";
  StdOutput = "blast_ncbi.out";
  StdError = "blast_ncbi.err"; 
  InputSandbox = {"aadnafra.fsa"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/blast"; 
  OutputSandbox = {"blast_ncbi.out","blast_ncbi.err"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/blast"; 
  Myproxyserver= "myproxy.ngs.ac.uk";
  Requirements = (      
       member("NGS-UEE-BLAST-NCBI", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  );
  ShallowRetryCount = -1;
  

• NGS Web Portal Submission

  After logging in to the NGS portal, select the "Blast" template under the " Bioinformatics" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  Eg To submit a Blast job use the following command (one line. You should not include the backslashes):

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
  '&(executable=/usr/ngs/BLAST-NCBI) \
  (arguments= blastall -p blastn -d est_hum -i aadnafra.fsa -a 1) \
  (jobType=single)(directory=/home/ngsxxxx/ncbi_blast)\
  (stdout=blast_ncbi.out)(stderr=blast_ncbi.err)'

  • The Working directory is set to /home/ngsxxx/ncbi_blast which must have been previously created and where ngsxxx is replaced by your unix id on ngs.rl.ac.uk
  • Stdout and Stderr are set to 'blast.out' and 'blast.err' respectively.
  • The first argument must be the program we want to run. (blastall in this case)
  • The input files must be given as argument and not as stdin .
  • The (executable=/usr/ngs/BLAST-NCBI) always points to the latest BLAST version, unless there is a version specification as a sufix, i.e., (executable=/usr/ngs/BLAST-NCBI_2_2_18) or (executable=/usr/ngs/BLAST-NCBI_2_2_16)

   

Searching Other Databases.

Both EBI EMBL Nucleotide and Uniprot Knowledgebase Protein databases are installed on all NGS nodes that support Blast and are updated regularly, as documented here. Instructions are given in the "Searching Other Databses" section of the Blast Toolbox page for how to search different parts of the database using standard blast commands. On the ngs.rl.ac.uk installation, there are also some shortcuts available.

Further Information

Documentation for NCBI BLAST can be found here.

The latest executables can be downloaded from here:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST

Blast Guide
Mailing List. NCBI mailing list for BLAST news.