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Genomic Region For Ncbi Transcript(/Gene) Accessions

I retrieved a lot of mRNA accession's and their genomic exon-intron structure via the Eutilities tool in perl and Bioperl, retrieving and parsing a genbankfile containing all results from the following query:

"Mus musculus"[orgn] AND "refseq"[Filter] AND "mrna"[Feature key]

Current problem is that I can only retrieve the contig-location (the location within each NT_..., NW...,... entries) while I need the genomic location of each exon. Any suggestions on how I can retrieve the genomic location of those contigs (with Eutilities and perl if possible)?

Thanks!

ncbi perl bioperl
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updated by Biostar Biostar • written by mluypaert • mluypaert

1 answer

If you want this for everything in the genome, why not just pick up the GFF3 file on the FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/

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written by deanna.church deanna.church

I discovered this file 2 days ago (via a colleague) and it seems that this is indeed exactly what I needed (I'm not very familiar with the ncbi data and GFF files yet so I missed them when I started my search). Thanks!

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written by mluypaert • mluypaert

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