[Bioperl-l] bl2seq

[Usha Rani Reddi]

Hi,
I am trying to compare two hundred thousand probes(each one of them) to
another genome. Format of the file containing probes is like this
SEQ_ID	PROBE_ID	POSITION	PROBE_SEQUENCE
NC_004116	1	1	AATTAACATTGTTGATTTTATTCTTCAACATC
NC_004116	3	13	TGATTTTATTCTTCAACATCTGTGGAAAACTT
NC_004116	5	25	TCAACATCTGTGGAAAACTTTATTTTTTTATG
NC_004116	7	37	GAAAACTTTATTTTTTTATGGTACAATATAAC
NC_004116	9	49	TTTTTATGGTACAATATAACAATAATTATCCA
NC_004116	11	61	AATATAACAATAATTATCCACAAGACAATAAG
NC_004116	13	73	ATTATCCACAAGACAATAAGGAAGAAGCTATG
NC_004116	15	85	ACAATAAGGAAGAAGCTATGACGGAAAACGAA
What I am trying to do is compare PROBE_SEQUENCE to fasta file of
Streptococcus agalactiae. I am trying to loop through the probes but not
sure how to proceed. My program is working fine for single sequence. One
more thing is I am not interested in matches, I want to display only
mismatches. I am new to Bioperl, some one please help me with this.
Thanks
Usha