PST: parallel simulation tool for studying tag-based database search

About PST

Tag-based database search has shown its superiority in identifying peptides with post-translational modifications (PTMs). Peptide backbones are identified in the procedure of tag-based database search without prior knowledge of potential PTMs. However, the required conditions for the correct identifications of tag-based database search are still unknown.

Here we implement a parallel simulation tool for investigating the necessary conditions of tag-based database search. We generate simulated spectra from database sequences and then search these simulated spectra to verify the correctness of inferred labels. Details about our simulation results are in the paper below.

Related Publication
J. Dai*, F. Yu*, N. Li, and W. Yu. *Contributed equally to this work.
"Is it feasible to only use tags in database search for PTM-invariant peptide identification? — A simulation-based study",
In The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017 Poster). Full paper in preparation.

Where to download PST

The binaries will be uploaded soon.

Environment configuration

Please install Python 3 and NumPy to use this tool.

How to use it?

The usage will be updated soon.