[Genome] in-silco PCR

[Ann Zweig]

Hello Demetra,

	There is no way to do this in a bulk manner using the website PCR tool. 
  However, the stand-alone, command-line tool is freely available for 
download and use by academic, non-profit and individual users.  This 
tool allows for bulk input files.

	From the usage statement:

~> isPcr
isPcr - Standalone v 33x7 In-Situ PCR Program
usage:
    isPcr database query output where database is a fasta, nib, or 
twoBit file or a text file containing a list of these files,  query is a 
text file file containing three columns: name, forward primer, and 
reverse primer,  and output is where the results go. The names 'stdin' 
and 'stdout' can be used as file names to make using the program in 
pipes easier.

	The isPcr tool is part of the blat suite of tools.  Read about how to 
download it here: http://genome.cse.ucsc.edu/FAQ/FAQblat.html#blat3


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


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Demetra Stamm wrote:
> Is there a fast way to import primer sequence data into in-silco PCR to get 
> the sequence data out for several primer sets without having to do it by 
> hand?
> 
> thank you for your help with this matter,
> 
> Demetra Stamm 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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