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 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.


  • Both programs are available from our FTP site

    For additional information about PrimOU or TM_By_PRIMO, contact

    Bruce Roe, broe@ou.edu or Steve Kenton, skenton@ou.edu.


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