[Gmod-help] gbrowse_syn

[Scott Cain]

Hi Jonathan,

I'm forwarding this email to the gbrowse mailing list and Sheldon.
Replies can trim help at gmod.org off the cc list.

Scott


On Wed, Mar 18, 2009 at 4:07 PM, Shao, Jonathan
<Jonathan.Shao at ars.usda.gov> wrote:
> Sheldon McKay,
>
>
>
> My name is Jonathan Shao and I believe I met you at PAG.  I saw your demo
> and  I am trying to implement the gbrowse_syn program.
>
>
>
> How do I generate meaningful clustal alignments?
>
>
>
> case 1: have contigs and want to align them to a completed genome
>
> Do you blast the contigs against the completed genome and then use clustalw
> on that isolated region?
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>
>
>
>
> case2: align 2 completed genomes
>
> Do you slice/cut up one of the completed genomes into defined sequence
> lengths and blast each sequence against a completed genome?
>
>
>
> Is blast the method of choice or are that other programs that would be
> better for aiding in creating the alignments for clustalW?
>
>
>
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>
> ##############################################################################
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> Do you have sample data with corresponding contig files that I can work
> with? I did see the wormbase gbrowse_syn, but I am not sure how you
> generated the alignments. Also, I did not see a sample config file for
> gbrowse_syn.
>
>
>
>
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> Any advice you can give me would be appreciated.
>
>
>
> Thanks in advance,
>
>
>
> Sincerely,
>
> Jonathan Shao
>
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research