[Genome] how to get the sequence flanking transcription start site

[Archana Thakkapallayil]

Hello Zhuo,

You could fetch the downstream sequences using the Table Browser. To get 
to this, click on the "Tables" link in the blue bar at the top of the 
Genome Browser page.  Then make the following selections in the Table 
Browser:

1. Set the clade, genome and assembly to the organism you are interested
2. group: Genes and Gene Predictions track
3. Then select the track and table that you are interested
4. region: genome
5. output format: sequence and click "get output"

Then choose "genomic" and hit "submit". On this page check only the box 
"Downstream by -- bases" and specify the number of bases downstream in 
the text box here. The default is 1000. Then hit "get sequence".

This gives you the fasta sequence of downstream regions for all the 
Genes in the table that you have selected.

Unfortunately, due to current high priorities, we won't be able to 
address your request at the current time. However, you could download 
sequence from our downloads server and process it off-line. The 
downloads server is here:

http://hgdownload.cse.ucsc.edu/downloads.html

Then you could use our tools from the Genome Browser source at,
http://genome.ucsc.edu/FAQ/FAQlicense#license3 or your own tools to 
manipulate the sequence.

Also, please see this previous mailing list question on getting genomic 
sequence from a program:
http://www.cse.ucsc.edu/pipermail/genome/2006-October/012008.html

I hope this information is helpful to you. If you have further 
questions, please do not hesitate to contact us again.

Regards,

Archana
UCSC Genome Bioinformatics Group


du zhuo wrote:
> Dear all
> I want to consult on you how to get the sequence flanking all the
> transcription start sites (TSS). We can conveniently get the 5000 bases
> upstream TSS in the download section of UCSC genome browser, but how can we
> get the downstream sequences? Additionally, could you provide the service
> for download the genome sequence using personalized parameter like the
> Ensemble genome browser did?
>
>