[Biojava-l] blast parser alignment middle line

Christian Gruber Christian.Gruber at biomax.com
Tue Apr 13 10:06:57 EDT 2004


Hello!

Is there a way to get the middle line of an alignment that I parse out 
of the blast output? In the example below, it would be the "S++VGTR..." 
line. In the Alignment of the SeqSimilaritySearchSubHit, I only find a 
Sequence entry for Query and Sbjct.

Query: 2 SFEVGTRCWYPHKELGWIGAEVIKNEFNDGKYHLEL...
          S++VGTR W P    GW+ +EV+K   +  K  L  ...
Sbjct: 4 SYDVGTRAWQPDPTEGWVASEVVKKTVDGNKVTLIF...


Thanks,
Christian


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