[Bioperl-l] display protein/CDS multiple sequence alignments with exon boundaries
cjfields at uiuc.edu
Wed Sep 5 08:53:25 EDT 2007
You mean something like this?
On Sep 5, 2007, at 4:42 AM, Albert Vilella wrote:
> A couple of examples:
> treefam has exon boundary and PFAM domain mappings
> here the tree is shown as well, but the idea would be to plot the
> 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,
> 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
>>>> 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:
>>> 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
>> Acc. to the Gbrowse tutorial GBrowse can deal with alignment data:
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