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Last update:
August 12. 2006 06:38:37
 

BLAST.PL

Description

This script uses BioPerl functions to align a group of nucleotide sequences against a BLAST-able database (created from formatdb.pl).  The result is a BLAST report for each query sequence as well as an output file out.txt.

Arguments

  • Fasta file containing the query sequences
  • BLAST Database Name
  • E-value cuttoff (All high scoring pairs (HSPs) with a score worse than this number will be removed ignored).
  • Boolean parameter specifying that the Database contains protein sequences.

Notes

Usage:
$./blast.pl -i seq.fasta
                  -d Pfa3D7_Annotated
                  -e 1e-10
Output:
  • out.txt
  • blast_QUERYNAME.out
*Ex: the output file for NC_004331-1410 would be "blast_NC_004331-1410.out"
 
 

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