Useful software from the Drinkwater Lab
Mstat was developed to help students analyze their data using nonparametric statistical methods. This program grew out of a graduate course, "Statistical Problems in Genetics and Molecular Biology," taught by the Department of Oncology at the University of Wisconsin-Madison over the last 30 years. In addition to performing a wide variety of nonparametric statistical tests, the software also provides simple routines for plotting data.
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.