Hi Liquo, Someone here also suggested that you could use the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) to get the information you needed by using the tables knownGene and knownGenePep:
1. Select the assembly of your choice. 2. Ensure that UCSC Genes is selected for track. 3. Ensure that the region selected is "genome". 4. Choose "selected fields from primary and related tables" as the output format. 5. Click "get output". 6. Choose knownGenePep from the list of Linked Tables, scroll to the bottom and click "Allow Selection From Checked Tables". 7. Select all the fields from knownGene as well as the seq field from knownGenePep. 8. Click "get output". 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 3/2/11 5:39 PM, Mary Goldman wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
