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: [email protected].
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<[email protected]> 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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