[Bioperl-l] extract nt positions from Hit

[Jason Stajich]

This sounds a little like homework - did you try to read the SearchIO HOWTO and give the example code in there a whirl?
http://bioperl.org/wiki/HOWTO:SearchIO

On Oct 4, 2012, at 2:30 PM, Rondon Neto <rondonbio at yahoo.com.br> wrote:

> Hi there!
> I would like to know if there is a way to recover the nucleotides and their positions in the database sequences that are divergent from query, by Search::IO.
> What I need are:
> - the nucleotides
> - their positions in DB sequences
> - the positions of mismatches and gaps that they are related.
> 
> thank you very much,
> 
> Rondon
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org