Hi! I've a multiple fasta file with a lot of nucleotide sequences in it. I made a blastx with this file against a database. Now I want to parse the blast result. To be more precisely: I want to get the translated protein query sequence with it's start and stop position for each hit. I am using the example code from the BioJava cookbook (http://biojava.org/wiki/BioJava:CookBook:Blast:Parser). The parsing works fine so far, besides one problem. I am able to get the start and stop position for the query sequence via hit.getQueryStart() and hit.getQueryEnd(). But I couldn't figure out yet, how to get the translated protein query sequence out of the blast result. I couldn't find something like hit.getQuerySequence() or similar. I would guess that something like that exists already somehwere or am I wrong and I've to implement it myself?
Thanks, Marcel _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
