Hi Liquo, Codons shown for the knownGene track are calculated as a user requests them - they are not being pulled from a database or file. However, you may be able to use the CDS FASTA alignment files from the Conservation track to get the information you need. The *.exonAA.fa.gz files here http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/alignments/ should have the information you need. The following help page should help you understand how these files are formatted: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 3/1/11 11:34 AM, liguo wang wrote: > Hi, > > What's the best way to get genome coordinates for a particular amino > acid? I believe UCSC should have this sort of data because UCSC > knownGene track can represent different amino aicd using a vertical > bar on the exon. > > For example, I want to get all the positions of Methionine throughout > the human genome. > Thanks you very much. > > -Liguo Wang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
