can not assign rev binding region correctly with provided fasta sequence

matdoering / openPrimeR

An R Package for Multiplex PCR Primer Design and Analysis

http://openprimer.mpi-inf.mpg.de

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can not assign rev binding region correctly with provided fasta sequence #3

Closed k1197445 closed 4 years ago

k1197445 commented 4 years ago

Hi I try to design both forward and reverse primers. With provided fasta sequence to assign binding region, fw binding region was resolved properly, but rev binding regions not.

below is the code I used: template = read_templates("MSI_template.fa", hdr.structure = "GROUP", id.column = "GROUP", delim = ">") template = assign_binding_regions(template, fw = "fw.bs.fa", rev = "rev.bs.fa")

FASTA sequence of template, binding regions are attached

fw.bs.fa.TXT MSI_template.fa.TXT rev.bs.fa.TXT

k1197445 commented 4 years ago

In many cases, the position of rev binding regions were assigned even upstream of fw binding regions.

matdoering commented 4 years ago

Thanks for finding this bug and the files for recreating it. I've just commited a change that should fix the issue: https://github.com/matdoering/openPrimeR/commit/5e4ef9e96265ac2df024986e4ffda1d6cf48d9a7

You should be able to get it working with the latest openPrimeR version on GitHub.