Hello Rajesh, To extract estimated promoter regions for the whole genome, select a track to base the analysis on (UCSC Genes, RefSeq Genes, etc.), then use the Table browser. Select output=sequence, sequence type=genomic, region=Promoter/Upstream by XXX bases (you decide the XXX). http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence
The first base in the region is XXX bases upstream from the transcription start site of the transcript in the track (as determined by genome alignment). The last base in the region would be one base before the transcription start site. Using hg18, there are a few tracks to consider. Starting at the Gateway page, select the genome hg18. Then use the button "configure" (instead of submit). The resulting page lists all tracks. Click on a track name to learn about the contents/methods. In this section "Configure Tracks on UCSC Genome Browser: Human Mar. 2006 (NCBI36/hg18)" use the button "expand all" to view all track. Starting tracks to consider are in the Regulation group. Click on tracks to see which fit your needs. Suggested tracks to start with are Eponine TSS, SwitchGear TSS, and possibly FirstEF. Tracks in the Pilot ENCODE Transcription group may also be helpful (although the data is restricted to the pilot regions). Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/23/10 6:08 AM, Venkata Rajesh Yella wrote: > Dear sir, > > your website is extremely useful for genome sequence extraction. > I have some queries on promoter extraction. > 1.what is the +1 position in promoter is it Transcription start > site or > Translation start site? > 2.How can i extract promoter sequences whole human genome at a > time, can > you suggest me any FTP site. > 3.where can i get experimentally verified TSSs and -1000 to +1000 > w.r.t > TSS > for humans. > > Thanks in advance, > > Rajesh, > Research student, > MBU, > IIsc. > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
