Hi Rebecca, Thank you for the additional information. I have several bits of information for you:
1. The display of the multiple alignment on the details page cannot be reverse-complemented; however, you can view the reverse complement on the main Genome Browser display page if you zoom to base level and use the "reverse" button. In this case, it is very helpful to go to the configure page and change the image width to a much wider image. 2. It is possible to export MAF data using the Table Browser. Hit the "Tables" link in the navigation bar at the top of the page, and select: clade: insect genome: D. melanogaster assembly: Apr. 2006 group: comparative genomics track: conservation table: multiz15way region: position (enter the region you would like to export) output format: MAF - multiple alignment format then hit "get output". You should get the alignments in the region you specified in MAF format, but they will not be reverse-complemented. 3. We do have tools that will reverse-complement the sequences in a MAF. They are part of the Kent source tree: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads and they are free for academic, noncommercial, and personal use. There are two tools that can reverse complement data from a maf track: 'mafFrag' and 'mafFrags'. To get reverse complemented sequence using mafFrag, you specify the coordinates and strand in command-line arguments. With mafFrags, you use a BED6-formatted input file with strand information. (BED format is described here: http://genome.ucsc.edu/FAQ/FAQformat#format1 .) Run either command without arguments to see a usage statement. Both tools work with database tables. You can use our public MySQL server to access the necessary tables by placing a file called ".hg.conf" in your home directory as described here: http://genome.ucsc.edu/FAQ/FAQdownloads#download29 You will also need the maf file from: http://hgdownload.cse.ucsc.edu/goldenPath/dm3/multiz15way/ . You can get the coordinates of your region of interest either from the window you are looking at in the Genome Browser (but subtract 1 from start -- see here: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1) or from the "FlyBase Genes" track. 4. There might be an alternative to using the Kent source tools for reverse-complementing MAF data available at the Galaxy website: http://main.g2.bx.psu.edu/ . Galaxy is run by our collaborators at Penn State and works in conjunction with the Genome Browser. According to this page: http://g2.trac.bx.psu.edu/wiki/MAFanalysis there is a tool to "Reverse complement a MAF file". If you have questions about Galaxy, you can contact them at [EMAIL PROTECTED] I hope this information is helpful. If you have further questions for us, please feel free to contact us again at [EMAIL PROTECTED] -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/03/08 13:31, Rebecca Beerman wrote: > thank you so much for getting back to me Brooke. I think I am more > interested in your scenario 2. I am looking at > http://genome.ucsc.edu/cgi-bin/hgc?o=5934390&t=5934730&g=multiz15way&i=multiz15way&c=chr3R&l=5934390&r=5934730&db=dm3&pix=620 > > <http://genome.ucsc.edu/cgi-bin/hgc?o=5934390&t=5934730&g=multiz15way&i=multiz15way&c=chr3R&l=5934390&r=5934730&db=dm3&pix=620> > > at: 12 Flies, Mosquito, Honeybee, Beetle Multiz Alignments & phastCons > Scores > > I'm interested in aligning the 5'UTR of drosophila fmr1 (CG6203) with as > many species as possible. The alignment provided is pretty good- > although I wish I could import the alignment into a program like > sequencer so I could move some of the sequences around a bit more. > (importing sequences directly into sequencer gave very poor alignment- > so I want to keep the alignment produced by USCS program) > Is there a way to export the alignment? > > thank you again for your time. > Rebecca > > On Nov 3, 2008, at 4:05 PM, Brooke Rhead wrote: > >> Hello Rebecca, >> >> Are you referring to viewing alignments on the main Genome Browser >> display page (http://genome.ucsc.edu/cgi-bin/hgTracks)? If so, the >> "reverse" button just below the main display (between the "configure" >> and "refresh" buttons) will flip the entire Genome Browser display and >> reverse complement sequence displayed when you are zoomed in to base >> level. >> >> If you are instead referring to alignments that are displayed when you >> click on a track and look at a details page, there is not an option >> supplied for reverse-complementing the view there. However, we have >> some tools that could help you generate the view you are looking for. >> If this is the case, which track are you trying to view? >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> On 11/03/08 06:14, Rebecca Beerman wrote: >>> I apologize if this question is answered somewhere on your site. >>> UCSC genome browser provided a great alignment of bp in the 5'UTR >>> of a Drosophila gene with other drosophilids. I want to see that >>> same bp alignment in the reverse and complement orientation so that >>> the gene reads 5' to 3', but I could not find that option for >>> configuring the alignment. I s this possible? or do I have to copy >>> each sequence and then re-align with a different program to see the >>> alignment in the 5'-3' oritentation? >>> thank you!! >>> Rebecca >>> Rebecca Beerman >>> Cellular and Molecular Biology Graduate Program >>> University of Pennsylvania >>> 540 Clinical Research Building >>> 415 Curie Blvd >>> Philadelphia, PA 19104 >>> work phone: 215-573-9386 >>> e-mail: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >>> _______________________________________________ >>> Genome maillist - [email protected] <mailto:[email protected]> >>> http://www.soe.ucsc.edu/mailman/listinfo/genome > > Rebecca Beerman > Cellular and Molecular Biology Graduate Program > University of Pennsylvania > 540 Clinical Research Building > 415 Curie Blvd > Philadelphia, PA 19104 > work phone: 215-573-9386 > e-mail: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > > > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
