How To Automate Primer Blast With Perl?

Question

[BioInfo1010]

Hey all!

does any one have a PERL script for automating the PRIMER BLAST tool.... i.e. i want a script which will submit my fasta file and parameters to Primer BLAST and retrieve the output. I'm stuck because I'm not able to code in the waiting period between submission and output receipt using mechanize.

Any help is greatly appreciated. Vikas

[Joseph Hughes]

Did you specifically want to use primer-blast? Or would you be alright using primersearch from EMBOSS?

Answer 1

[Lee Katz]

There's a program by Jim Kent called isPCR that gives the PCR product, given two primers.

http://genome-test.cse.ucsc.edu/~kent/exe/linux/isPcr.zip

Otherwise, command line blastn with a small word size should work.

[BioInfo1010]

Thanks for ur answers. Actually, I don't have primer sequence but I want to design primers using Primer BLAST.

Thanks,

Answer 2

[Lee Katz]

If you want to design primers, then use primer3

web - http://primer3.wi.mit.edu/

CLI - http://primer3.sourceforge.net/releases.php