[Bioperl-l] Genome location of sequences

Jonathan Manning bmb9jrm at bmb.leeds.ac.uk
Wed May 19 18:31:57 EDT 2004


Thanks for the replies. I'm actually writing this as part of a utility
to be used by non-specialists, the idea being that all they have to do
is submit a query string/accession and wait. So anything requiring a
manual input-like downloading chromosomal coordinates from websites
might be out of the question - I'll try the BLAST location idea.

Having said that, extrapolating from another recent posting, maybe LWP
would work for the genome browser form? How easy/ useful is that? Sorry
if I'm edging a bit off-topic from Bioperl.....



On Wed, 2004-05-19 at 20:44, Barry Moore wrote:
> 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.
> Barry
> 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
> >genome?
> >
> >Cheers,
> >
> >Jon
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >  
> >

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