EuGenoSuite

EuGenoSuite is the extension of GenoSuite multi-algorithmic analysis core to enable eukaryotic proteomics searches. In EuGenoSuite, proteomic analysis features relevant to Eukarytotic gene models like protein inference(important to analyze transcriptomic data where isoforms will have shared peptides) are added on top of the peptide searches and result integration. Features like protein level FDR calculation and result filtering is also added to this application.

This command line application can be used as an indepent proteomic data search tool for peptide and protein identification using OMSSA and X!Tandem algorithms. It can also be integrated to Eukaryotic proteogenomic pipelines to enable peptide identifications from extra-large genomic and transcriptomic databases.

Executables will be provided for windows and linux platforms and requires OMSSA and X!Tandem to be already installed.

A README file provides information about setup and usage.

To use EuGenoSuite you need OMSSA and X!Tandem to be installed, A protein fasta to search against, MGF spectra files in a directory, a config file to define path for input files and a parameter file to define parameters for the search.

No separate installation step is required for the EuGenoSuite itself. Simple unarchiving the .zip should enable the executables to be used. In linux you might need to provide permissions and probably dos2unix of fasta and MGF files.