[Bioperl-l] Fasty frameshift-characters

[Jason Stajich]

I think I strip it out because Bio::LocatableSeq objects don't know what
to do with them.  You can get it from
$hsp->query_string and $hsp->hit_string depending on if you are doing
fasty or tfasty.

-jason
On Fri, 21 May 2004, TAPO (Thomas Agersten Poulsen) wrote:

> Dear BioPerl list,
>
> 	I am using Bio::SearchIO(-format=>"fasta") to parse the output
> from FASTY, but I do not get the frameshift-characters ('/' and '\') in
> the sequences returned by
> next_result->next_hit->next_hsp->get_aln->each_seq->seq(). This is
> apparently independent of what 'missing_char' is set to.
> 	Please, can anybody help me recover the frameshift information?
>
> Sincerely
> Thomas Poulsen
>
> -----------------------------------------------------
> Thomas A Poulsen       Research Scientist, PhD, MSc
> Novozymes A/S           Protein Design / Bioinformatics
> Brudelysvej 26, 1US.24  Phone: +45 44 42 27 23
> DK-2880 Bagsværd.       Fax:   +45 44 98 02 46
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu