Thanks, that was just what I was looking for. Andrew
On Fri, Apr 9, 2010 at 12:46 AM, Brooke Rhead <[email protected]> wrote: > Hello Andrew, > > The gbCdnaInfo table links the Genbank accession number to the CDS > information you are looking for. The CDS info is in the 'name' field of the > table 'cds'. The relationship is: > > gbCdnaInfo.acc --> gbCdnaInfo.cds = cds.id --> cds.name > > To get the information with the Table Browser, select the gbCdnaInfo table > and paste a list of mRNA identifiers. You will need to strip the version > number (the ".1") off first. Choose "output format: selected fields from > primary and related tables". Hit "get output", select the cds.name field, > and hit "get output" again. You should see a result like this: > > #hg19.gbCdnaInfo.acc hg19.cds.name > NM_001014431 341..1783 > > Please let us know if you have any further questions by replying to the > list at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > Andrew Yee wrote on 4/8/10 8:25 PM: > >> Hi, I was trying to find a table that corresponds to the mRNA information >> in >> Genbank. >> >> Take for example, the entry for NM_001014431.1 in >> http://www.ncbi.nlm.nih.gov/nuccore/62241012. I'd like to find a table >> where the coordinates correspond to the numbers listed in the Genbank >> entry. >> I'd like the coordinates to be given with respect to the transcript. For >> example, it shows the CDS go from 341..1783. However, the tables I've >> found >> so far at UCSC (e.g. refGene) correspond to the genomic coordinates. >> >> Thanks, >> Andrew >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
