software for Insilico Pcr

Question

[moohit21]

Hello Friends, I hope u all are doing good. I have desgined primers using primer_3_core and i have obtained 70,000 primer pairs, now i want to do the insilico pcr of these primers, can anybody told me any good software for insilico pcr, i am using ubuntu operating system. Any command based application would me much more appriciable, or any script.

Thanks in advace.

[moohit21]

@kevin.. Thanks for your answer, but how i am going to put 70,000 primer pairs in it, it is showing the space for only 1 primer pair

[Kevin Blighe]

See at the bottom of the page to which I have linked you:

In-Silico PCR was written by Jim Kent. Interactive use on this web server is free to all. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available. Contact Jim for details.

Jim'll fix it for you.

It is also possible to programmatically engage with web-forums via, for example, shell scripts, but I would not recommend it in this case as it may break UCSC's 'good use' policy.

Answer 1

[Kevin Blighe]

Try the University of California, Santa Cruz's (UCSC's) in silico PCR tool: https://genome.ucsc.edu/cgi-bin/hgPcr

Kevin