Hello Kevin, You can get an alignment of the species in our conservation track for any given assembly using our table browser (http://www.genome.ucsc.edu/cgi-bin/hgTables). Depending upon the output format you want there are two ways to approach this problem. To get the output as a custom track in the browser, after selecting your assembly of interest (for this example I'll use human, Mar. 2006) select:
group: Comparative Genomics track:Conservation table: phastCons28wayPlacMammal region: click position and input: chr1:9134313-9134423 (note that you must use this coordinate format) output format: custom track (you could also get the data points or bed formatted data this way) then click on "get output". This will take you to a menu where you can choose to display the custom track in the genome browser or table browser or to get it as a file. If you want a maf, select instead: group: Comparative Genomics track:Conservation table: multiz28way region: click position and input: chr1:9134313-9134423 output format: MAF - multiple alignment format. Hopefully this information was helpful is enough to get you started. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Kevin1 wrote: > Dear Mr. or Miss., > > I am a graduate from East China Normal University and I am now studying how > transcription factors activate microRNA expression. Could you please tell me > how to create alignment of specific fragements using your table browser? And > you can use this as an example: Chromosome 1, position 9134313-9134423. > Thank you for your time! I'm really looking forward to your kind reply. > > Best regards, > Kevin > 11-11-08 > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
