Question: Genomic Region For Ncbi Transcript(/Gene) Accessions
1
gravatar for mluypaert
6.0 years ago by
mluypaert10
Belgium
mluypaert10 wrote:

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 • 1.5k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 6.0 years ago by mluypaert10
3
gravatar for deanna.church
6.0 years ago by
deanna.church1.1k
Bethesda, MD
deanna.church1.1k wrote:

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/

ADD COMMENTlink written 6.0 years ago by deanna.church1.1k

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!

ADD REPLYlink written 5.9 years ago by mluypaert10
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