Software
GenoSuite: Large scale mass spectrometry based proteomics experiments can be utilized to annotate protein coding regions in a genome, which traditionally is annotated with in silico approaches and contain errors in gene boundaries. GenoSuite is an automated pipeline for such proteogenomic reannotation of prokaryotic genomes. It is a command line utility which analyzes tandem mass spectra against a genome translated database with four open-source peptide identification algorithms and enables discovery of novel genes and correction of erroneous gene boundaries. It is a ready to use executable and can be downloaded for common computer operating systems; Windows, Linux and Debian.
If GenoSuite is helpful to your research, please consider citing following reference.
EuGenoSuite: Similar to GenoSuite, EuGenoSuite is a proteogenomic analysis tool but for complex eukaryotic genomes. EuGenoSuite is the proteomic search component of our pipeline and searches spectral data with OMSSA and X!Tandem algorithms against custom proteogenomic database. It integrates multi-algorithmic searches with FDRscore (Jones et al. Proteomics 2009) calculation and protein grouping post peptide detection. In tandem to RNA-seq based custom proteogenomic database creation, EuGenoSuite can be a useful application enabling eukaryotic genome annotation. It can be downloaded from here.
If EuGenoSuite or related research is helpful to your research, please consider citing following reference.