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

Chris Fields cjfields at uiuc.edu
Wed Sep 5 08:53:25 EDT 2007


You mean something like this?

http://www.bioperl.org/wiki/HOWTO_Discussion:Graphics

chris

On Sep 5, 2007, at 4:42 AM, Albert Vilella wrote:

> A couple of examples:
>
> http://www.treefam.org/cgi-bin/alnview.pl?ac=TF105041
>
> treefam has exon boundary and PFAM domain mappings
>
> http://www.ensembl.org/Homo_sapiens/genetreeview?gene=ENSG00000139618
>
> here the tree is shown as well, but the idea would be to plot the  
> alignment
>
> So it's more "show me the multiple CDS/protein alignment" rather  
> than "show
> my aligned CDS/proteins wrt my reference genome"
>
> I think it would be quite neat to have this as a bioperl howto,
>
> Comments?
>
>     Albert.
>
> On 9/4/07, Chris Fields <cjfields at uiuc.edu> wrote:
>>
>>
>> On Sep 4, 2007, at 9:31 AM, Jay Hannah wrote:
>>
>>> On Aug 31, 2007, at 4:29 AM, Albert Vilella wrote:
>>>> Probably a bit of a long shot but does anyone have code for
>>>> displaying protein or CDS multiple sequence alignments with the  
>>>> exon
>>>> boundaries of each gene in the alignment?
>>>>
>>>> Something in the bioperl world without funky external dependencies.
>>>> I think
>>>> it would be an awesome addition to the howtos.
>>>>
>>>> Currently, the Bio::Graphics howto has cdna to genome mapping
>>>> scripts or
>>>> blast output scripts, but
>>>> I couldn't find code for dealing with multiple sequence alignments.
>>>
>>> I'm currently under the (potentially uninformed) impression that
>>> Bio::Graphics and related tools only work with a single  coordinate
>>> system. I've never seen a multiple sequence alignment example.
>>>
>>> (
>>>    I Google'd for "gbrowse alignment" and hit this:
>>>    http://maizeapache.danforthcenter.org/cgi-bin/gbrowse.cgi
>>>
>>>    Click the second Example link and you'll see exons mapped out.
>>>
>>>    But zooming all the way in with all the tracks turned on it looks
>>> like the AZM tracks are just the coding regions. I don't see any
>>> multiple sequence alignment...
>>> )
>>>
>>> I doubt that helped.  :)
>>>
>>> Jay Hannah
>>> http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah
>>
>> Acc. to the Gbrowse tutorial GBrowse can deal with alignment data:
>>
>> http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-
>> Browser/docs/tutorial/tutorial.html
>>
>> chris
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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