[Bioperl-l] Conversion of contig coordinates to chromosome

Jonathan Manning bmb9jrm at bmb.leeds.ac.uk
Sun Jun 20 05:43:42 EDT 2004

Hi all,

This is kind of mixed Ensembl API/Bioperl question, so I've posted to
both lists.

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

Is there a way to 'project' contig coordinates onto a chromosome without
using ensembl? I could then extract from Ensembl using the 'chromosome'
coordinate system. I only really need all the features for human
sequences, which seem to work okay (though I'd like to have the
information available in other organisms anyway), so downloading an
entire NCBI contig in order to extract the subsequence is an option, but
I'd rather not, since the files are big and it would take a while
(permanent local storage not an option).

Any suggestions appreciated.


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