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

Florent Angly florent.angly at gmail.com
Fri Aug 24 12:07:04 EDT 2007


Thanks for all the replies.

Sendu Bala wrote:

> Isn't Bio::Assembly::Contig what you need?
>
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Assembly/Contig.html
>
I'm using this module already to manipulate the contigs, but there's no
option that I know of to _display_ the contigs in the way I described.
(Sorry, the title of my email was misleading.)


De-Jian,ZHAO wrote:
> How do you pad the sequences with gaps manually? Just replace the
> hyphens with blanks? If yes, you can program in perl to automate
> this process.
>   
How do I pad the sequences manually?? I calculate how many gaps have to
go left and right of the aligned sequence based on its length, its
position in the aligned consensus and the consensus length.
my $newseq = '-' x $leftnum . $seq . '-'x$rightnum
By the way, the sequences cannot be stored with blanks in them...

I think the best way to provide an out-of-the-box solution for
displaying contigs the described way would be to _not_ use Bio::Align at
all, but rather to create a new assembly IO module like
Bio::Assembly::IO::simpleout for example. That would be useful.

The reason I wanted to visualize these contigs is because I made a
Bio::Assembly::IO module for TIGR Assembler files that I intend on
submitting to BioPerl. I wanted to make sure first that I did not have
any obvious bug in my contig coordinates. I've read the documentation on
the Wiki so if a BioPerl developer would please like lo step up and
contact me directly for checking my code, that would be nice =)

Florent


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