[Genome] Question

[Brooke Rhead]

Hello Sujana,

We have several online tools for finding sequence within the human genome:

1. BLAT - This is useful for locating sequences that are at least 40 
bases in length.  Access the tool by clicking the "Blat" link in the 
blue bar at the top of our web page.  Information and instructions on 
using BLAT are available here:

http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

BLAT is probably the tool you are looking for.  However, there are two 
more tools you might find useful for slightly different kinds of searching:

2. Short Match - This tool is for locating short sequences (2-30 bases 
in length) within a particular region of interest.  To access it, go to 
the main Genome Browser Gateway page 
(http://genome.ucsc.edu/cgi-bin/hgGateway), select the genome you are 
interested in (likely Human Mar. 2006, the latest human assembly) and 
hit "submit".  Scroll down to the "Mapping and Sequencing Tracks" 
section and look for the blue "Short Match" link.  Follow the link to 
enter a sequence and change the display mode to "full".

3. PCR - A third tool is our PCR tool, located here:
http://genome.ucsc.edu/cgi-bin/hgPcr?command=start (or by clicking the 
"PCR" link in the blue bar at the top of the page).  This tool is 
somewhat like BLAT, but it is more useful for locating PCR primers.

I hope this information helps.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Sujana Raval wrote:
> Hi,
> I was using your genome website for some research , I was wondering if there was any tool online that I could use to search the whole Human Genome for a particular sequence pattern.I would really appreciate your help.
> Thank you
> Sujana
> 
> 
> Sujana Raval
> Biomedical Engineering
> University of Southern California
> 
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