[Bioperl-l] parse Blast Output and Composition Based Statistics
hubert.prielinger at gmx.at
Thu Jan 12 18:57:16 EST 2006
I want to know, if there is a possibility to get from a Blast Outputfile
the whole Sequence of a protein not only the best local alignment...
>ref|XP_480077.1| hypothetical protein [Oryza sativa (japonica
dbj|BAD33542.1| hypothetical protein [Oryza sativa (japonica
Score = 24.1 bits (47), Expect = 493
Identities = 6/7 (85%), Positives = 7/7 (100%), Gaps = 0/7 (0%)
Query 2 KKRRRWW 8
Sbjct 87 KRRRRWW 93
and now, if I parse the file, I want to get the whole Sequence of this
hypothetical protein....is that possible with hsp for example, or any
my second question is:
I do my blast search with bioperl and the remoteblast module.....each
parameter is working very well, except the composition based statistics
it looks like that:
my $factory =
it should work like that, but it doesn't....
Thanks for your help in advance......
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