Thanks very much for the information. I'll have a look at the track control page for the Conservation track. Best wishes, Ruth
Brooke Rhead wrote: > 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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
