inquires about in-silico PCR on local machine

[Kim, Panjun]

To whom it may concern,

I am a PhD student at the University of Tennessee Health Science Center.

I tried to find how to install and use in-silico PCR on my local machine, but it was hard to get them.

Could I get some information on how to install and use it stand-alone type because there are too many primers to test to use them through web-based in silico pcr.

Thank you.

Sincerely,

Panjun

[Daniel Schmelter]

Hello Panjun,

Thanks for writing in about a high-throughput version of isPCR and for your patience with this response.

We have the isPcr utility download available for Linux computers here:

http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/

As with all of our utility programs, this is a pre-compiled binary that needs execute permission to run. You can enable this in the appropriate directory with the following command:

chmod +x isPcr

You can run the program without arguments to see an instructional usage statement:

~$ ./isPcr 
isPcr - Standalone v 37x1 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.
options:
   -ooc=N.ooc  Use overused tile file N.ooc.  N should correspond to 
               the tileSize
   -tileSize=N the size of match that triggers an alignment.  
               Default is 11 .
   -stepSize=N spacing between tiles. Default is 5.
   -maxSize=N - Maximum size of PCR product (default 4000)
   -minSize=N - Minimum size of PCR product (default 0)
   -minPerfect=N - Minimum size of perfect match at 3' end of primer (default 15)
   -minGood=N - Minimum size where there must be 2 matches for each mismatch (default 15)
   -mask=type  Mask out repeats.  Alignments won't be started in masked region
               but may extend through it in nucleotide searches.  Masked areas
               are ignored entirely in protein or translated searches. Types are
                 lower - mask out lower cased sequence
                 upper - mask out upper cased sequence
                 out   - mask according to database.out RepeatMasker .out file
                 file.out - mask database according to RepeatMasker file.out
   -makeOoc=N.ooc Make overused tile file. Database needs to be complete genome.
   -repMatch=N sets the number of repetitions of a tile allowed before
               it is marked as overused.  Typically this is 256 for tileSize
               12, 1024 for tile size 11, 4096 for tile size 10.
               Default is 1024.  Only comes into play with makeOoc
   -noSimpRepMask Suppresses simple repeat masking.
   -flipReverse Reverse complement reverse (second) primer before using
   -out=XXX - Output format.  Either
      fa - fasta with position, primers in header (default)
      bed - tab delimited format. Fields: chrom/start/end/name/score/strand
      psl - blat format.

This tool is owned by Kent Informatics and is free only for non-commercial use, for other uses please contact Jim Kent. Hope that tool can help with your primers! Let us know if you run into problems.

All the best,

Daniel Schmelter
UCSC Genome Browser

For further communication, please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.

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