james.wasmuth at ed.ac.uk
Tue Aug 23 04:13:56 EDT 2005
How new are you to Perl?
I would turn these probe sequences into a fasta file using Bio::SeqIO.
Use this as the input file for a normal blast search.
Then search the blast output using Bio::SearchIO.
The best way to learn is with the HOWTOs:
any problems? Post back to the list.
hope this helps
Usha Rani Reddi wrote:
>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.
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
"You have made your way from worm to man,
and much in you is still worm."
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Blaxter Nematode Genomics Group |
Institute of Evolutionary Biology |
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