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- Title
MultiPhATE2: code for functional annotation and comparison of phage genomes.
- Authors
Zhou, Carol L. Ecale; Kimbrel, Jeffrey; Edwards, Robert; McNair, Katelyn; Souza, Brian A.; Malfatti, Stephanie
- 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.
- Subjects
WIKIPEDIA; COMPARATIVE genomics; LINUX operating systems; GENOMES; BACTERIOPHAGES; SEARCH algorithms; ANNOTATIONS; DATABASE searching
- Publication
G3: Genes | Genomes | Genetics, 2021, Vol 11, Issue 5, p1
- ISSN
2160-1836
- Publication type
Article
- DOI
10.1093/g3journal/jkab074