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