[Bioperl-l] re trieving blast multiple alignment in fasta form

[Dave Messina]

Hi Eric,

Wait, do you want multiple pairwise alignments in your output FASTA file,
or a single multiple alignment of your query and all the hits?

If the former, get_aln() will give you one pairwise alignment per hsp, but
you'll need to move the output file creation statement (my $alnIO = ...)
before the loops so it gets created only once. Then, when you do the write
statement ($alnIO->write_aln($aln);), all of the alignments will go to the
same file.

If on the other hand you'd like to have a multiple alignment between a
query and all of its hits, you'll have to take the IDs of the hits, pull
the corresponding sequences out of the database, and then run a multiple
alignment algorithm on them.


Dave