Hi Peter,

Sorry about that, I did a double check and you are right, the tool doesn't "screen" sequences. Maybe try BLAT itself to identify then clip? It depends on how long your primers are - shorter than 20 will need some tuning. Ask UCSC directly (Galt) about how to configure for this type of match: gen...@ucsc.edu.

Best,

Jen
Galaxy team

On 2/8/11 2:23 AM, Peter Cock wrote:
On Tue, Feb 8, 2011 at 3:46 AM, Jennifer Jackson<j...@bx.psu.edu>  wrote:
Hello Peter,

If these are standard length PCR primers, then UCSC's In-Silico PCR tool
would be an option. It is a varient of BLAT and the source is available from
Kent Informatics. Here is a UCSC link to the online version (send Jim Kent
an email for a copy):

http://genome.ucsc.edu/cgi-bin/hgPcr?command=start

A wrapper could be made for your own instance or just use it command-line
before loading data. If this is not what you had in mind, please let us
know,

Best,

Jen

Thanks Jen,

If I've understood the purpose of the UCSC's In-Silico PCR tool it is for
predicting the PCR product of a given primer pair and genome sequence.
That's now quite what I have in mind - more like EMBOSS' primersearch
- but I'm sure would be useful at some point.

Peter

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
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