Bioperl-guts: Results parsing and alignments

Aaron J Mackey ajm6q@virginia.edu
Wed, 30 Jun 1999 12:16:03 -0400 (EDT)


I'm at the point with the Search::Processor::* stuff that I need to deal
with generating alignment objects.  I'm not entirely sure how to use
Bio::SimpleAlign when I have Seq data (it seems to be geared towards file
I/O).

For instance, I can deduce (i.e. regex match) the query and hit sequences
that align, the range over which they align, and the "match" symbols
present (if any).  How do I package this up into a SimpleAlign object?  Do
I just create two Seq objects of equal width, and then (somehow) pass them
to SimpleAlign's constructor? (The code doesn't seem to support this
option - just use addSeq()?)  How would Seq.pm know about the range?

Optionally, Bio::Search::Hit::* objects could retain alignment information
in some other fashion (sequences, range information and arrays of gap
positions) and include methods akin to those of SimpleAlign for generating
textual representations for display/saving.  Please advise.

Thanks!

-Aaron

-- 
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\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
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 \  amackey@virginia.edu    /
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