[Bioperl-l] Bioperl-l Digest, Vol 89, Issue 19

Dave Messina David.Messina at sbc.su.se
Tue Sep 28 03:58:00 EDT 2010

> Any one can tell how to use the make_primers.pl script?
> What is Coordination file?

>From the documentation at the top of the script:

Description: This program designs primers for constructing knockouts
of genes by transformation of PCR products (ref: Datsenko & Wanner,
PNAS 2000).

A tab-delimited file containing ORF START STOP is read, and primers
flanking the start & stop coordinates are designed based on the
user-designated sequence file.

In addition, primers flanking the knockout regions are chosen for PCR
screening purposes once the knockout is generated.  The script uses
Bioperl in order to determine the primer sequences, which requires
getting subsequences and reverse complementing some of the objects.


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