[Bioperl-l] Genome Scanning Question

[Sean Davis]

On Thu, Sep 17, 2009 at 8:31 PM, Michael UNO <mwachholtz at unomaha.edu> wrote:

>
> What objects & methods could be used if I wanted to determine if a gene is
> located at a specific location within a genome at the Ensembl database. For
> example, if given a coordinate (e.g. Canine Chr15:66,500,123) is there a
> method that will simply tell me "yes, there is a gene at this location".
> And
> can it tell what gene(s) are located at this coordinate?
>

There are a number of ways to go about this.

If you want to go with perl, object-oriented, and ensembl, check out:

http://www.ensembl.org/info/docs/api/core/core_tutorial.html

If you want to start with tab-delimited text files, check out downloading
the text files from the UCSC genome browser.

Sean



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