[Bioperl-l] Genome location of sequences

Barry Moore barry.moore at genetics.utah.edu
Wed May 19 15:44:01 EDT 2004

We've used UCSC Genome Browser for this.  Use the table menu to download 
the chromosomal coordinates for the RefSeq mRNA entries, then use their 
DAS server to get the spliced sequence from coordinates, or download a 
local copy of the chromosome, and do the splicing yourself.


Jonathan Manning wrote:

>Hi all,
>I want to be able to locate any GenBank-derived sequence to a position
>on the genome. The reason for this is that I have installed the Ensembl
>API and wish to access detailed information on variation etc (which I
>don't think is possible with bioperl????). Trouble is that I don't seem
>to be able to access things on ensembl by a GenBank ID- at least not for
>the mRNAs I'm using as an example. 
>So: is there a way to lock a genbank sequence down to its position on a
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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