README.md

METATRYP v. 1.1 Documentation

These tools are intended to help researchers answer questions about proteomics data. Written in Python 2.7 and implemented on a Unix operating system (linux/macOS).

The METATRYP software consists of:

1. a database, stored in a standalone SQLite file.
2. python libraries, for processing, ingesting, and analyzing data.
3. command-line scripts, to act as interfaces to the python libraries and the database.

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• Overview
• Installation Instructions
  • Download
  • Create virtual environment
  • Run tests
  • Initialize database
• Quick Usage Guide
  • Digest and ingest new taxa
  • Generate peptide redundancy tables
  • Remove taxa from database
• Tutorial
  • List Taxa in Database
  • Generate a Redundancy Table
  • Query for Peptides in Taxa
  • Make a New Database
  • Taxa in Example Database
• Database Schema
• Directly query database via SQL

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For higher volume instance of the METATRYP software with additional features (like Lowest Common Ancestor Analysis), please see METATRYP v. 2(https://github.com/WHOIGit/metatryp-2.0). A web portal using a marine microbe database can be found at https://metatryp.whoi.edu/, and a portal using a coronavirus focused database can be found at https://metatryp-coronavirus.whoi.edu/.

When using METATRYP v. 1 please cite the following:
Saito, M.A., Dorsk, A., Post, A.F., McIlvin, M.R., Rappé, M.S., DiTullio, G.R. and Moran, D.M. (2015), Needles in the blue sea: Sub‐species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome. Proteomics, 15: 3521-3531. doi:10.1002/pmic.201400630