MultiPhATE2: code for functional annotation and comparison of phage genomes
Abstract
To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Mar 17, 2021
- Source ID
- 10.1093/g3journal/jkab074
Entities
People
- Brian A Souza
- Carol L. Ecale Zhou
- Jeffrey A Kimbrel
- Katelyn McNair
- Robert A Edwards
- Stephanie Malfatti
Organizations
- Flinders University
- Lawrence Livermore National Laboratory
- San Diego State University
- United States Department of Defense
- United States Department of Energy