[Bioperl-l] bl2seq

[James Wasmuth]

Hi Usha,

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:
http://bioperl.org/HOWTOs/html/SeqIO.html
http://bioperl.org/HOWTOs/html/SearchIO.html

any problems? Post back to the list.

hope this helps

james


Usha Rani Reddi wrote:

>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
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>  
>

-- 
"You have made your way from worm to man,
    and much in you is still worm."
	Friedrich Nietzsche, Thus Spoke Zarathustra


Blaxter Nematode Genomics Group   |
Institute of Evolutionary Biology |
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