[Bioperl-l] what format is this and how I can use AlignIO

[Jason Stajich]

We currently don't have a parser for sim4 as alignments - we handle sim4
as an exon identifier see Bio::Tools::Sim4::Results for more info.

I bet it wouldn't be terribly hard to make an alignio module using our
existing parser.


-jason
On Mon, 25 Feb 2002, Guoneng Zhong wrote:

> Hi,
>
> Sorry for the ignorance on this matter.  I am trying to use the output
> of this standalone program called sim4 to create some sort of Alignment
> object.  The output looks like the following.  I thought perhaps BioPerl
> can give me an object that tells me exactly which nucleotide matches
> with which across the two aligned strands (that's what AlignIO does,
> right?).
>
>
> seq1 = sim4seq4HyyX8K.seq, 2460 bp
> seq2 = sim4seqOD34cJI.seq ((no header)), 876 bp
>
>
> (complement)
>
>        0     .    :    .    :    .    :    .    :    .    :
>     1567 TGACAAGAGCACTGGCAAGGAGAACAAAATCACTATCACTAATGATAAGG
>          ||||||||||||||||| |||||-|| ||||||||||  |   |  | |
>        1 TGACAAGAGCACTGGCATGGAGA CAnAATCACTATCmcTanyGayAmGs
>
>       50     .    :    .    :    .    :    .    :    .    :
>     1617 GTCGTCTCAGCAAGGAGGACATTGAGCGCATGGTGCAGGAAGCTGAGAAG
>          | ||||||||||||||||||||||||||||||||||||||||||||||||
>       50 GtCGTCTCAGCAAGGAGGACATTGAGCGCATGGTGCAGGAAGCTGAGAAG
>
>      100     .    :    .    :    .    :    .    :    .    :
>     1667 TACAAGGCTGAGGATGATGTGCAGCGTGACAAGGTTTCTGCCAAGAACGG
>          ||||||||||||||||||||||||||||||||||||||||||||||||||
>      100 TACAAGGCTGAGGATGATGTGCAGCGTGACAAGGTTTCTGCCAAGAACGG
>
> Any help?
>
> Thanks,
> G
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu