M.H.S. Capstone Project

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"