Hello Lisa, The Conservation track is where can examine the conserved, orthologous genome regions in the Browser. You also can view all other aligned data with it: UCSC Genes, RefSeq Genes, Other RefSeqs (RefSeqs from other species - possibly be ortholog gene candidates)).
To extract data is a bit of a more lengthy procedure, but once you use the tools, it will seem straightforward for future queries. *Viewing Data:* To view the genomic alignments, open the Assembly browser in the Human Feb. 2009 (GRCh37/hg19) assembly, and enter your coordinates and submit. One the next page, adjust the tracks as desired by opening and closing display with the pull-down menus. Suggestions: Conservation, UCSC Genes, RefSeq Genes, Other RefSeq. Click on each track name in order to filter the display (select/de-select species) and adjust sub-tracks and view the methods, credits, source. *Extracting Data:* To extract data for a region (in Table Browser): 1) set the track to Conservation, table to multiz46way 2) region = your coordinates 3) output as MAF and check the "Galaxy" box 4) get output This will send the data over to Galaxy where you can filter the MAF down to the exact region of interest (the Table browser extracts the entire block(s) that overlap with your specified region). With Galaxy you can also extract fasta sequence from the MAF by species. (This is all done with web tools. If you would prefer to use unix tools on the command line, write back for help in that direction). Go back to UCSC using the Get Data -> UCSC Main link in Galaxy or just go back to the UCSC Browser, both are the same. Create a master interval MAF file of your region (in Table Browser): 1) Set track = assembly, table = gold, set region 2) select output as BED and check Galaxy Box 3) get output The next form does not really apply for this track (one region per gene, etc), but you can change the custom track name if you want. 3) submit To filter larger MAF block by region (in Galaxy): 1) Fetch Alignments -> Extract MAF blocks 2) Choose intervals: your custom track 3) MAF Source: Alignments in your history 4) Choose alignments: the Conservation MAF block that you originally sent over 5) Execute To get fasta from MAF (in Galaxy): 1) Convert Formats -> MAF to Fasta 2) Select Dataset, choose species 3) Execute Export/download result, or send back to UCSC, or do more things in Galaxy. Help links are on both the Table browser page and the Galaxy page -> See top tool bar in both. We hope this is helpful, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/27/10 12:53 PM, Pfeifer, Lisa (NIH/NIMH) [V] wrote: > Hello, > > I would like to know how to view the orthologous regions for a section of > human chromosome 3 in all nonhuman primates for which sequence data is > available (rhesus macaque, mouse lemur, marmoset, etc.). The region in > question is about 20 kb. I want to be able to scroll along the region and > compare the sequences among species at the base pair level. I also want to > download the nonhuman primate DNA data in FASTA format and input it into > another file where I have human data. > > Thank you, > Lisa Pfeifer > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
