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

[Chris Fields]

Updated the page on the web site with the new script.

Figured it out; if you pass the parameter -label_position 'left' it  
will display the label to the left.  However it displays them right  
next to the segment (ala GBrowse).  I added a hack to  
Bio::Graphics::Glyph::generic in CVS which allows 'alignment_left' as  
an option, displaying it aligned to the far left of the panel; there  
is probably a way to use a callback here as well.

chris

On Sep 5, 2007, at 8:31 AM, Albert Vilella wrote:

> Awesome!!
>
> Thanks Chris!
>
> On 9/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
>>
>> 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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>>>>
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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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign