[Bioperl-l] Raw Blast Alignment
Simon K. Chan
simon_sask at yahoo.com
Tue May 9 04:06:04 EDT 2006
Hi Fellow Bioperl-ers,
supposed to show the raw alignments using
Bio::SearchIO. The script is written to parse a
PSI-BLAST report. I found an old email in the archive
from Jason stating that this should parse other
flavors of blast reports as well.
What do I need to do to make this script parse non-PSI
blast reports? I tried to just specify a file and
that the -format is 'blast', but I get an error
stating that the object method 'raw_hit_data' is not
defined in Bio::Search::Hit::BlastHit.
Basically, I want to obtain the raw alignment because
I'd like to get the size of the gaps, not just the
Any help will be much appreciated.
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
More information about the Bioperl-l