Hello, The cds data is obtained from NCBI directly, it is part of the genbank record as submitted. It will likely be the same or similar to the browser alignment.
The all_mrna table has the alignment coordinates - for both the query mRna and the genomic sequence. The table is in PSL format http://genome.ucsc.edu/FAQ/FAQformat#format2 Here is some coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Valer Gotea (NIH/NLM/NCBI) [E]" <[email protected]> wrote: > From: "Valer Gotea (NIH/NLM/NCBI) [E]" <[email protected]> > To: [email protected] > Sent: Friday, November 27, 2009 10:20:48 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Mapping transcript CDS to genome > > Dear friends, > > I have a short questions related to the mapping of CDSes for genBank > transcripts onto the genome assembly (hg18 in this case). > > I would be curious to know how exactly the position of CDS start and > CDS > end are mapped onto hg18 for the transcripts included in the > "gbCdnaInfo" table. For example, BC051699 has transcript mapping info > in > "all_mrna" table, and is linked to CDS ID 105093 in the "gbCdnaInfo" > table, which in turn indicates the CDS being "140..1471" in the "cds" > table. I am not sure where to find the info on where the 140 and 1471 > coordinates in the transcript are mapped onto the genome, so I would > appreciate some help clarifying that. > > Thank you in advance, > Valer > > -------------------------------- > Valer Gotea > Research Fellow > CBB / NCBI / NLM / NIH > http://www.ncbi.nlm.nih.gov/CBBresearch/Fellows/Gotea/ > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
