Passing Fasta File To Primer3

Question

[New_Perl_Guy]

Hi,

I have a perl program which allows me to browse NCBI database for particular gene sequence and return the gene sequence as a fasta file. now I want to pass the sequence to primer3 (I would like to design primer for the sequence). So can anyone help we with any perl scripts which allow me to call primer3 website and use the fasta file as input?

Thanks

Answer 1

[Pierre Lindenbaum]

Rather than creating a robot, you'd better install the standalone version of primer3.

Regarding the script fasta2primer3, I found the following perl code : http://www.koders.com/perl/fid1E5D858FC135163F31E3BF1855BD4E62DA641547.aspx?s=open#L2

at the end your pipeline should work like this:

cat sequence.fasta | fasta2primer3.pl | primer3 -format_output > result.p3

[Michael Schubert]

I think the correct unix way would be fasta2primer3.pl < sequences.fasta | primer3 -format_output > result.p3 (since there is no concatenation involved), but that is really just nit-picking

[suani.pm]

Vous pouvez me donner le script pour convertir à fasta en primer3, je ne peux pas le trouver dans le link,

merci