Orphaned Peptide Finder App

Purpose

The Orphaned Peptide Finder (OPF) enables the comparison between peptide lists (as csv) and protein databases (as fasta). This allows the identification and output of peptides which are not present in the protein database, primarily the identification of peptides which were identified in a proteomic approach applying a six-frame translated database of Open Reading Frames (ORFs). These can then be used to improve genomic annotations (proteogenomics). OPF is fast, simple, and reliable as well as protein digestion method independent.

Run the program

To run the program, download and doubleclick the jar-file from the project root.

Build from sources

Requirements

• JDK 1.8
• Maven 3.3.9

To build the project with maven:

mvn clean package

A jar with the suffix jar-with-dependencies will be created in the target/ folder.

This can be executed on the command line:

java -jar target/orphan-peptide-finder-1.0.0-jar-with-dependencies.jar