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

[mwilkinson]

I don't know if this will be useful or not...

Genquire used to have a Sim4 GUI, which parsed the output and displayed the
alignment against the genome sequence.  It's pretty archaic, and we haven't
included it in the final release of Genquire, but the code is still hanging
around on my hard drive.

No promises of functionality, and the Genquire "overhead" will have to be
pulled out to make it functional, but if you think it would be remotely useful
to you I can send you the module as soon as I get back from the hackathon.

Mark


Jason Stajich wrote:

> 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
>
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