[Bioperl-l] parse Blast Output and Composition Based Statistics parameter

Hubert Prielinger 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...
for example:

 >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 
other way....

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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