[Bioperl-l] Genome location of sequences

Sean Davis sdavis2 at mail.nih.gov
Wed May 19 20:42:08 EDT 2004


Depending on how much use and how much "batch" querying you will be doing,
you can fairly easily set up a GFF relational database and load the
chromosome data into it.  You can then do "local" slice-like queries.  You
can also load features if you have them in GFF format.  See Bio::DB::GFF for
some examples of what you can do.


On 5/19/04 18:31, "Jonathan Manning" <bmb9jrm at bmb.leeds.ac.uk> wrote:

> Hi, 
> 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.....
> Cheers,
> Jon
> 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
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