Re: gbrowse_syn help for a unique scale

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Re: gbrowse_syn help for a unique scale

Sheldon McKay
Hi L.BRIGITTE,

I am sorry for the delayed response.  GBrowse_syn tries very hard to
render the different species on the same scale but this is not easy if
the species are not closely related.  The more co-linearity among
species the closer the scale because the whole screen is taken up by a
single contiguous segment for each species.  This falls apart if the
relationships are more distant, as only aligned regions are shown and
the alignments tend to be smaller and more sparse for distant
relatives.  One way you might mitigate this is to select the alignment
chaining option to on by default via your configuration file.  This
option will group smaller aligments into bigger meta-alignments.


Sheldon

Sheldon McKay, PhD
Engagement Team Scientific Lead,
iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204


> From: l.brigitte <[hidden email]>
> Date: Mon, May 3, 2010 at 3:52 AM
> Subject: [Gmod-gbrowse] gbrowse_syn help for a unique scale
> To: [hidden email]
>
>
>
> Hello,
>
> I work in INRA Versailles and I’m using Gbrowse_syn for my studies.
>
> I’d like to visualize conserved regions of three different species. Could
> you tell if it is possible to have them with the same scale?
>
> I hope I was clear enough and do not hesitate to contact me if you need more
> details.
>
>
>
> Best regards,
>
> L.BRIGITTE
> --
> View this message in context:
> http://old.nabble.com/gbrowse_syn-help-for-a-unique-scale-tp28433725p28433725.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
>
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