Peppy: a fully integrated, proteogenomic mapping software tool. Peppy generates a peptide database from genome files, tracks peptide loci, matches peptides to MS/MS spectra, assigns scores to those matches, and tracks score distributions to find E-Values. To determine false discovery rate thresholds, Peppy automatically generates a decoy database from the original genome files and repeats the entire search process. Peppy is written in Java for cross-platform execution, and is fully multi-threaded for enhanced speed.
Peppy Spectrum Visualizer: a tool for creating visual representations of PKL/DTA files.
HMM_Score: HMM_Score is a platform for the scoring and identification of peptides by tandem mass spectrometry (MS/MS). It has very high accuracy because it takes into account several spectral characteristics gleaned from large data sets, including the mass distribution of peaks, the intensity distribution of peaks, and the likelihood of fragmentation given the adjacent amino acids.
PIE-Web: PIE-Web is the user-friendly front-end web application for the Protein Inference Engine (PIE).
GFS: Genome-based peptide fingerprint scanning. Use this software to match MS and MS/MS data to a genomic sequence, available for open source download, or online use. Presently the download version is ready for Mac OS X only. However, we have an internal version that runs on Debian Linux and is currently being tested and packaged. Expect a Windows version to soon follow. We would love to hear from you if you are using GFS!
Basefinder/Shapefinder: Originally developed on the NeXT platform starting in 1991 and later brought to Mac OS X, this software is used for signal processing and base calling for DNA sequencing traces from either slab gels or capillaries. We have also applied it to the analysis of SHAPE data as well.
PROCLAME: The protein cleavage and modification engine. This software is for predicting possible combinations of post-translational modifications on intact proteins, using an intact mass measurement and a protein sequence from a database. It uses a search bounded by fuzzy-logic based constraints.
Francisella-FUGUE: Gene function prediction by alignment of gene sequence and protein structure profiles.