Hi DeQuincy, Adding the "frames" variable to a custom MAF track, will display the amino acids within coding regions. This variable has to point to a frames table that exists on the current assembly. For hg19, this table would be "multiz46wayFrames".
About the MAF format: the multiple alignment format stores a series of multiple alignments in a format that is easy to parse and relatively easy to read. This format stores multiple alignments at the DNA level between entire genomes. For more information see: http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Here is an example MAF custom track with the frames variable (note there is a small bug that is being fixed soon, but for now, you have to have a blank line after the last data line): browser position=chr1:229,586,268-229,586,355 track name=nup133 type=maf frames=multiz46wayFrames visibility=pack ##maf version=1 a score=5294057.0 s hg19.chr1 229586267 88 + 249250621 TTACCTCATCAATATATTCCAACAAGTCCAAAGCTTTCTTGAAATCATATTCATTAGCTCTTCTATTTTCTTCACAGATATATAGCTA s panTro2.chr1 210034299 88 + 229974691 TTACCTCATCAATATATTCCAACAAGTCCAAAGCTTTCTTGAAATCATATTCATTAGCTCTTCTATTTTCTTCACAGATATATAGCTA i panTro2.chr1 C 0 C 0 s ponAbe2.chr1 209727282 88 - 229942017 TTACCTCATCAATATATTCCAACAAGTCCAAAGCTTTCTTGAAATCATATTCATTAGCTCTTCTATTTTCTTCACAGATATATAGCTA i ponAbe2.chr1 C 0 C 0 a score=-8023.0 s hg19.chr1 229586355 12 + 249250621 TGACAAGTTAAA s panTro2.chr1 210034387 12 + 229974691 TGACAAGTTAAA i panTro2.chr1 C 0 C 0 s ponAbe2.chr1 209727370 12 - 229942017 TGAGAAGTTAAA i ponAbe2.chr1 C 0 C 0 Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 11/15/11 10:27 AM, DeQuincy Prescott wrote: > Hi guys, > > How do you create a track for Amino Acids? > > Here is a session with Amino Acids in the Conservation track. Would like to > be able to create a track with changes to Amnio Acids that we find due to > Next Gen Sequencing results. > > How do you get the Amino Acid code in the middle of the displayed block? > > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Qnc&hgS_otherUserSessionName=Amino_Acid_download > > ------------------------------------------------------------- > DeQuincy Prescott > Sen Res Tech to Professor Bhattacharya > ----------------------------------- > about our group > http://tinyurl.com/3264vn > ------------------------------------ > Mobile: +44 (0) 7590 695 435 > Office: +44 (0) 207 608 6951 > ------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
