[Bioperl-l] alignment and assembly

[Jason Stajich]

On Tue, 19 Feb 2002, Guoneng Zhong wrote:

> Hi,
> I am trying to write an alignment function and an assembly function for
> dna sequences.  I looked at the the Bio::Align modules and am not sure
> how they can help me.  I am used to seeing two sequences align with bars
> indicating that nucleotide on the top sequence matches with that in the
> lower sequence.  Is there a tutorial or example like that on the site?
>

See the Bio::AlignIO for how to read in alignments from files.  We don't
interface with phrap or the tigr assembler at this point.  Happy to see
someone design the appropriate objects that extend the Bio::SimpleAlign
object (via the Bio::Align::AlignI interface) to handle assemblies.  We're
happy to help with the object design if you lay out your plan.

> As for assembly, is there something like the TIGR Assembler that allows
> me to input two sequences and get hopefully one sequence out?
> (Obviously, I an make command line calls to TIGR Assembler, but perhaps
> a Bioperl interface?).
>
> Thanks,
> Guoneng
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu