Hi Ruth, One other thing that might be helpful for you to know is that the ORF displayed in the conservation track is based on gene annotations (described on the conservation details page). You can't change the ORF translation that is displayed; however, you can change the display so that it only shows the nucleotides. To do this, go to the track control page by clicking the blue "Conservation" track name, then go to the "Multiz Alignments Configuration" box and change the codon translation option to "No codon translation". Then you will be able to see the conservation of the methionine codon in the conservation track.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 04/29/10 15:06, Mary Goldman wrote: > Hi Ruth, > > You can always reverse complement the strand by pressing the reverse > button at the top of the track groups, which will also reverse > complement the conservation track. You can also complement the strand by > pressing the arrow button (--->) at the top of the base position track > (when you are zoomed in to at least the base level). However it is > important to realize that due to the strict base pairing of DNA, the > conservation of one strand is equivalent to the conservation of the > other strand. In other words, you do not need to reverse complement your > strand in order to see the conservation for a base. > > 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 4/29/10 8:30 AM, Ruth Bennett wrote: >> Hi, >> I am looking at a region on human chromosome 11 around the loci SLC22A18 >> & SLC22A18AS. >> There is a potential ORF for the locus SLC22A18AS which codes for 40aa >> (MENCMKRQRSAVCPHPSPPGLQLVGTGFCGCRGLPQILPH*) and I wanted to check the >> conservation of the first methionine. >> How can I change the conservation track to show me the conservation of >> the other strand as it currently only shows the conservation of SLC22A18 >> in this area (VLAATELTCLFMQFSIVP)? >> I would be grateful for any help. >> Kind regards. >> Ruth Bennett >> >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
