Hello all, this is my first time posting here and hopefully I am doing everything correctly. I am an IT guy who has been thrown into a position where I am learning bioinformatics... I would like to quickly and easily find/design overlapping primers for large multi-fasta files/sequences. Unfortunately, I am primarily working with windows (though I do have access to a few nix boxes), and while I have gotten primer3plus to work, it does not support overlapping primers, and I have been unable to get batchprimer3 to work (spent a few days messing with perl/apache, and editing the .pm/.cgi files)
Does anyone have any experience designing multiple overlapping primers with multifastas on windows that can give me some pointers?
I am open to new (free, non-webbased) sw propositions as well.
The only thing I have managed so far was to create an awk script to format multifastas for primer3 input... but still no overlapping abilities...
I greatly appreciate any guidance for the newb!
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sis.clayton •
" it does not support overlapping primers": well, you could use a high value for PRIMER_NUM_RETURN http://primer3.wi.mit.edu/primer3web_help.htm#PRIMER_NUM_RETURN
Wouldn't that also return largely overlapping primer pairs? My goal was to only have 20bp or so overlap and target ~700bp length, and do so in an automated fashion that wouldn't require hand selection of primer pairs from a list (a few thousand sequence multifasta)
or you could do a loop: find a pair of primers,exclude the region for the two primers (http://primer3.wi.mit.edu/primer3web_help.htm#SEQUENCE_EXCLUDED_REGION ), search again....
Oh hey Dr. Lindenbaum! Thanks for the suggestion about looping, probably the route I will go. (also thanks for the awk input, with a little modification, I got it working just fine)
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