[Bioperl-l] display protein/CDS multiple sequence alignments with exon boundaries

Chris Fields cjfields at uiuc.edu
Tue Sep 11 18:40:55 EDT 2007


On Sep 11, 2007, at 4:15 PM, Jay Hannah wrote:

> Lincoln Stein wrote:
>> You can view a simple multiple alignment now. Go to www.wormbase.org
>> <http://www.wormbase.org>, turn on some of the EST tracks and then
>> zoom down to base pair level.
>>
>> In bio::graphics, use the "segments" glyph and turn on the
>> -draw_target option. The features must have DNA attached to them.
>
> Wow.  *http://tinyurl.com/yuz8bq*   I hadn't seen that done before.

There is a section detailing how this is done in the GBrowse tutorial  
(though it uses older GFF):

http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome- 
Browser/docs/tutorial/tutorial.html

>> What's coming soon is support for MAF format, which provides
>> genome-level alignments.
>
> I'm looking forward to trying to wrap my head around that.  :)
>
> Jay Hannah
> http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah

It's easily parsible, which is nice!

chris


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