[Bioperl-l] Re: Conversion of contig coordinates to chromosome

Graham McVicker mcvicker at ebi.ac.uk
Sun Jun 20 09:03:22 EDT 2004

On Sun, 20 Jun 2004, Jonathan Manning wrote:

> I've been using the bioperl remoteblast module to locate sequences to
> the genomes of humans, and other organisms. I then use the resulting
> contig coordinates (I didn't have much luck searching the NCBI
> 'chromosome' database for non-human sequences) to retrieve high-quality
> information via the contig coordinate system of ensembl, which I can
> then 'project' to get chromosomal coordinates. I thought this was
> working well, but have found that not all NCBI contigs are listed in
> ensembl.

Hi Jonathon,

Can you give an example of an NT contig which is not in the ensembl human
database?  If the contig is part of the NCBI34 assembly then we ought
to have it in the homo_sapiens_core_22_34d database. 



Graham McVicker
EMBL - European Bioinformatics Institute
Cambridge CB10 1SD, UK
Tel: +44 (0)1223-492584
Fax: +44 (0)1223-494468

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