Thanks. That's definitely helpful. On Mar 3, 2011, at 1:09 PM, Mary Goldman wrote:
> 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 liguo wang [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
