[Bioperl-l] Is it possible to do contig alignments?

[Sendu Bala]

Florent Angly wrote:
> Dear list members,
> 
> I would like to "produce" an alignment of a contig, or more exactly 
> visualize it in a such a fashion based on the aligned sequences provided 
> to be by a sequence assembler:
> 
> Consensus: ACGTACGTTG
> Sequence1: ACG-AC
> Sequence2:  CGTACGT
> Sequence3:     AC-TTG
> 
> It sounds like a very trivial task but after searching for a long time, 
> it seems impossible using the methods BioPerl provides.

Isn't Bio::Assembly::Contig what you need?

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Assembly/Contig.html