Version 3.0.1 of mPrime has been released. This new version is a major re-write of mPrime using J 8.0.1 and the Qt toolkit. The latter eliminates the requirement for Java on OSX and Linux. In addition, primer3 and bowtie have been updated to versions 2.3.5 and 1.0.0, respectively. Although usage of mPrime is very similar to earlier versions, see the Help file for more information.
The bowtie indexes have been updated to Ensembl 71.
The bowtie indexes for cDNAs have been updated to Ensembl 69. No changes were required for the whole genome and chromosome indexes.
Version 2.6.2 of mPrime has been released. Minor changes to account for the new mouse assembly (GRCm38) in Ensembl 68. Run Check for updates from the Help menu.
All of the bowtie indexes have been updated to version 68 of Ensembl.
The mPrime software package provides a front-end for primer3, a widely-used open source program (http://primer3.sourceforge.net) for choosing oligonucleotide primers for polymerase chain reaction (PCR). In addition, it uses Bowtie (http://bowtie-bio.sourceforge.net) to rapidly identify potential mispriming sites within a particular genome. For any given primer pair identified by primer3, all sites in the genome with up to a user-specified number of mismatches, as well as potential PCR products, are identified by Bowtie. The Tm for each priming (or mispriming) site is computed by mPrime using the nearest-neighbor method. This information should facilitate making better choices of primers for PCR, cloning, or DNA sequencing. Target sequences may be imported into the program from fasta files, extracted from compressed fasta files that, for example, include an entire chromosome sequence, or downloaded from an Ensembl DAS Reference Server.
mPrime was written in J (Version 6.02), an Array Programming Language developed by JSoftware, Inc., and runs on Windows, OSX, or Linux.