[Bioperl-l] Conversion of contig coordinates to chromosome

[Jonathan Manning]

Thanks Haibo. I'm using the remoteblast.pm module, so I guess that's the
most recent build. 

For the benefit of the list, I've solved the problem. Apparently the
it's because I'm using a non-reference contig. The solution will be to
reject Blast hits from such contigs. 

Thanks for the help,

Jon

On Mon, 2004-06-21 at 14:33, hz5 at njit.edu wrote:
> Hi Jon,
> This file is mapping contig coordinates to chromosome locations.
>
ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/maps/mapview/BUILD.34/seq_contig.md.gz
> 
> haibo
> //cheers
> P.S. which build are you using? 34 should be pretty standard
everywhere
> 
> Quoting Jonathan Manning <bmb9jrm at bmb.leeds.ac.uk>:
> 
> > 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
> > ensembl.
> > 
> > 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.
> > 
> > Jon  
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> 
> =========================================================
> Haibo Zhang, PhD student
> Computational Biology, NJIT & Rutgers University
> Center for Applied Genomics, PHRI
> http://afs13.njit.edu/~hz5
>