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FORMATDB.PL

Description

This is a wrapper script around the formatdb program provided by NCBI with the command-line BLAST.  The wrapper script is needed to create user-friendly
    names for the sequences in the database.

Arguments

  • Fasta file containing sequences to be converted into a BLAST-able database. 

Notes

Usage:
$./formatdb.pl <Pfa3D7_WholeGenome_Annotated_CDS_2005.2.11.fasta
Output:
  • Pfa3D7_Annotated.nhr
  • Pfa3D7_Annotated.nin
  • Pfa3D7_Annotated.nsd
  • Pfa3D7_Annotated.nsi
  • Pfa3D7_Annotated.nsq

*These files are used by BLAST and should be placed in your BLASTDB directory (see the NCBI website for instructions on setting up BLAST).  If you choose not to do so, you must explicitly specify their location when running the blast.pl script.
 
 

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