The PrimOU Primer Picking Program and TM_BY_PRIMO, a TM calculating program derived from Primo.
PRIMOU is a version of the PRIMO program developed at the Genome Center at University of Texas - South West Medical Center which has been modified at the University of Oklahoma to fix memory leaks and handle multi-megabase projects such as our bacterial genome sequencing projects.
The major functional change we added to Primo was to insure all primers picked were unique by pre-screening against either a single contig or the entire sequencing project target contig set. This was done by adding -local and -global flags.
The -local flag screens against only the single contig which contains the primer.
The -global contig screens against the entire contig set to ensure that primers are unique to the whole project.
The use of these options prevents picking primers which would multiple prime, especially off our large (ca. 2Mbp) bacterial genomic projects.
We also have found it advisable to raise the quality for bases in primers set in the .cri file from 20 to 30 because the data with a quality of 20 is not completely accurate and has the possiblility of an inaccurate base in the primer picked that can cause mispriming and/or multiple priming.
TM_BY_PRIMO is a derivative program that computes the TM for a list of primers using the same algorithm as PRIMO. The input format is a set of name, sequence pairs one per line (with no spaces) that can be uses as MerMade input files.
