MultiPhATE2: code for functional annotation and comparison of phage genomes

Carol L. Ecale Zhou; Jeffrey Kimbrel; Robert Edwards; Katelyn McNair; Brian A. Souza; Stephanie Malfatti

doi:10.1093/g3journal/jkab074

MultiPhATE2: code for functional annotation and comparison of phage genomes

Carol L. Ecale Zhou, Jeffrey Kimbrel, Robert Edwards, Katelyn McNair, Brian A. Souza, Stephanie Malfatti

College of Science and Engineering

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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.

Original language	English
Article number	jkab074
Number of pages	5
Journal	G3 (Bethesda, Md.)
Volume	11
Issue number	5
Early online date	17 Mar 2021
DOIs	https://doi.org/10.1093/g3journal/jkab074
Publication status	Published - May 2021

Bibliographical note

Funding Information:
This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344.

Funding Information:
This work was funded by the United States Department of Defense, Defense Threat Reduction Agency grant number DTRA13081-32220 and the United States Department of Energy Office of Biological and Environmental Research award numbers SCW1632 and SCW1656.

Publisher Copyright:
© 2021 Genetics Society of America. All rights reserved.

Keywords

bacteriophage
bioinformatics tool
comparative genomics
gene prediction
genome annotation
phage

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Zhou_MultiPhATE2_P2021Final published version, 432 KBLicence: CC BY

Cite this

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title = "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.",

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author = "{Ecale Zhou}, {Carol L.} and Jeffrey Kimbrel and Robert Edwards and Katelyn McNair and Souza, {Brian A.} and Stephanie Malfatti",

note = "Funding Information: This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. Funding Information: This work was funded by the United States Department of Defense, Defense Threat Reduction Agency grant number DTRA13081-32220 and the United States Department of Energy Office of Biological and Environmental Research award numbers SCW1632 and SCW1656. Publisher Copyright: {\textcopyright} 2021 Genetics Society of America. All rights reserved.",

year = "2021",

month = may,

doi = "10.1093/g3journal/jkab074",

language = "English",

volume = "11",

journal = "G3: Genes, Genomes, Genetics",

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AU - Souza, Brian A.

AU - Malfatti, Stephanie

N1 - Funding Information: This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. Funding Information: This work was funded by the United States Department of Defense, Defense Threat Reduction Agency grant number DTRA13081-32220 and the United States Department of Energy Office of Biological and Environmental Research award numbers SCW1632 and SCW1656. Publisher Copyright: © 2021 Genetics Society of America. All rights reserved.

PY - 2021/5

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N2 - 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.

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MultiPhATE2: code for functional annotation and comparison of phage genomes

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