MultiPhATE2: code for functional annotation and comparison of phage genomes

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

doi:10.1093/g3journal/jkab074

MultiPhATE2: code for functional annotation and comparison of phage genomes

Journal Article · Wed Mar 17 00:00:00 EDT 2021 · G3

DOI:https://doi.org/10.1093/g3journal/jkab074· OSTI ID:1862740

Ecale Zhou, Carol L. ^[1]; ^[1]; Edwards, Robert ^[2]; McNair, Katelyn ^[3]; Souza, Brian A. ^[1]; Malfatti, Stephanie ^[1]

Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Flinders Univ., Bedford Park, SA (Australia); San Diego State Univ., CA (United States). Computational Sciences Research Center; San Diego State Univ., CA (United States); San Diego State Univ., CA (United States). Viral Information Inst.
San Diego State Univ., CA (United States). Computational Sciences Research Center

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: Defense Threat Reduction Agency (DTRA); USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1862740

Report Number(s):: LLNL-JRNL-814913; 1023357

Journal Information:: G3, Journal Name: G3 Journal Issue: 5 Vol. 11; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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comparative genomics
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References (29)

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