CycloNovo is a new algorithm that identifies spectra generated from cyclopeptides in large mass spectrometry datasets. CycloNovo can also de novo sequence the cyclopeptides represented by identified cyclospectra.
Developed in University of California San Diego, La Jolla, CA, USA
Dependencies (add binaries to PATH):
- NPDtools (https://github.com/ablab/npdtools)
System requirements:
- Linux or macOS
- Python 2.7
- GNU sed
To configure/test run:
make Makefile
Usage examples:
cyclonovo -s data/surugamide_spectrum.mgf -o test_output \
--denovo -k 5 --verbosity -e 0.015 --kmer_threshold 2
For the full list of available options please run
cyclonovo -h
Output:
- cyclonovo_classification_report.txt: list spectra analyzed with scores related to identifying cyclospectra
- cyclonovo_cyclospectra.mgf: mgf file contaning found cyclospectra
- cyclonovo_sequencing_reconstructions.txt: reconstructions if de novo sequencing option is used
For the latest version and the web application see (GNPS account necessary): https://gnps.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22CYCLONOVO%22%7D
For the latest development version see: https://github.com/bbehsaz/cyclonovo_dev
CycloNovo is available under a modified Apache 2.0 License, and is free for non-profit use.