[BiO BB] Re:Synonomous SNP finding

[Chris Moy]

> Jicheng,

> You can use sequence analysis packages to do the same thing. There are 
> those of the commercial variety like Sequencher. That will allow you 
> to load a reference sequence and compare a set of other sequences 
> (sequenced or otherwise) and identify variability in the sequence. 
> This will allow you to view the electropherogram as well (if 
> sequencing).  There is public software such as Consed available at the 
> Univ. of Washington that can run on unix platforms. You need do not 
> necessarily need to be working with sequencing data to use these 
> tools.

Chris

>
On May 19, 2004, at 12:01 PM, 
bio_bulletin_board-request at bioinformatics.org wrote:

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> Today's Topics:
>
>    1. Synonymous SNP finding (Jicheng Hao)
>
> --__--__--
>
> Message: 1
> Date: Tue, 18 May 2004 14:36:38 -0700
> From: "Jicheng Hao" <jhao at tgen.org>
> To: <bio_bulletin_board at bioinformatics.org>
> Subject: [BiO BB] Synonymous SNP finding
> Reply-To: bio_bulletin_board at bioinformatics.org
>
> I have used MUMmer to find SNPs between an incomplete genome and its
> reference completed genome.  I then use Artemis manually to find
> synonymous SNPs by studying genes on the reference genome.
>
> I wonder if there is an automatic way(tool) to conduct Synonymous SNP
> finding. Otherwise,  I have to write a tool to do that.
>
> Thank you.
>
> Jicheng Hao, Ph.D.
> Staff Scientist, Bioinformatics
> Comparative Genomics Unit
> Pathogen Genomics Division=20
> Translational Genomics Research Institute (TGen)=20
> 602 343 8705 (phone)
> 480 570 5969 (mobile)
> 602 343 8740 (fax)
> jhao at tgen.org
>
>
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