Hello Olga, For a single SNP, there is a quick method for a similar result:
1) open genome browser for target assembly 2) set the position to display just the SNP 3) hide all tracks except for the SNP track 4) click on "DNA" in top blue navigation bar 5) add in the 200 bases up and down stream 6) set other formatting options if desired 7) click on "extended color/case options" 8) the SNP track will come up as a track that you can add some special formatting to (underline, change case, etc.) 9) submit for fasta sequence You can have other tracks open at step #3 to have them as options at step #8. You can also extract SNPs and flanking sequence using rs identifiers in the Table browser. In this type of batch query, adding in annotation notations to the resulting fasta sequence based on other tracks is not possible (exception = repeats). http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#BatchQuery Hopefully you find this tool helpful, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/12/10 10:26 AM, Olga Likhodi wrote: > Dear community, > > Could you tell me how to obtain the flanking sequence of a SNP (200bp > upstream and downstream) > > With the other SNPs masked as N's when I have the rs number? > > Thank you for your help, > > Olga > > > > Olga Likhodi, MSc. > Pharmacogenetics Research Department > Clarke Institute of Psychiatry > Centre for Addiction and Mental Health > 250 College St. R-50 > Toronto, ON CANADA > Phone: (416) 535-8501 ext. 4572 > > > > > ______________________________________________________________________ > This email has been scanned by the CAMH Email Security System. > ______________________________________________________________________ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
