script for local blast to mapped primer to the genome

Question

[skdv2522]

hey everyone i want to write a Perl or bioperl script to run the blastn in order to mapped the primer sequence on to the whole genome... please help me write the script . it would be very helpful for me. thanks in advanced

[barslmn]

What is your question?

[skdv2522]

i have SRR based primer sequence with SRR sequence information. i have to locate these primer with SRR region between them on the genome. for this particular task i have to write perl script. this is going to be in 2-3 steps. first i have to concatenate the forward primer and reverse primer with 25N NUCLOTIDE BETWEEN them. then i have to perform local blast

[Joe]

Please do not add comments as answers.

Biostars is also not a coding service, we will help you with the script, but you need to show what you have attempted so far - we will not write it for you.

Evidently you understand the steps you require, so you need to start writing the code.