These tools are intended to help researchers answer questions about proteomics data. Written in Python 3.6 on a Unix operating system (linux/macOS).
Some specific questions that these tools help provide answers for include:
- Is tryptic peptide XXX found in Proteome A and Proteome B?
- How many tryptic peptides do Proteome A and Proteome B have in common?
- Are tryptic peptides XXX and YYY both found in Proteome A?
- How many tryptic peptides are there in Proteome A that differ from peptide XXX by n positions?
- What is the Lowest Common Ancestor of taxa containing peptide XXX?
METATRYP v. 2.0 has faster performance and higher throughput than METATRYP v. 1.0 which it is based upon. A web server instance of METATRYP v. 2.0 using a marine microbe database can be found at https://metatryp.whoi.edu/, and a web instance using a coronavirus focused database can be found at https://metatryp-coronavirus.whoi.edu/.
METARYP 2.0 now supports the ingestion and search of Genomes, Metagenomes and Metagenome Assembled Genomes (MAGs) and calculation of the Least Common Ancestor (LCA) for each peptide. This repository is designed both to be used as a stand-alone application and in support of the Ocean Protein Portal (https://proteinportal.whoi.edu).
The METATRYP software consists of:
- a database, stored in a standalone postgreSQL database.
- python libraries, for processing, ingesting, and analyzing data.
- command-line scripts, to act as interfaces to the python libraries and the database.
When using METATRYP v. 2.0 please cite the following: