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primer mismatching software/sites

primer mismatching software/sites - PCR - Polymerase Chain Reaction Forum

primer mismatching software/sites - PCR - Polymerase Chain Reaction Forum. Discuss and ask questions about PCR troubleshooting, PCR protocols and methods, PCR products, and PCR theory.


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Old 02-09-2007, 04:00 PM
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Angry primer mismatching software/sites



where I can find a software or a website in which I can blast my primers (rat) and have back the possible mismatching?
I already used BLAST from Ensembl and NCBI and FASTA but they return a lot of false positive, are time consuming (average of 3 minutes each primer), do not allow to search for both primers in the same moment...
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Old 02-10-2007, 09:50 AM
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Default Re: primer mismatching software/sites

Hello Tlaragio!

Not sure exactly what you want to BLAST against.

I have some programs that I used:

virtual PCR (where you enter primer sequences)
[Only registered users see links. ]

If you have used Perl before, Perl Primer can BLAST primers you design in the program:
[Only registered users see links. ]

For Linux (A Perl 5 interpreter or higher on a Linux system is required.), Oligo Picker BLASTs your primers in NCBI
[Only registered users see links. ]

Cheers!

Last edited by moleculardude; 02-10-2007 at 09:52 AM.
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