SEA-PHAGES | New annotation software

Link to this post \| posted 10 Jan, 2022 23:24
ptsourkas	Hello everyone, I would like to introduce Phage Commander, a new genome annotation tool developed in our lab. Phage Commander is designed to make genome annotation with multiple gene calling programs easier, faster, and less error prone. While DNA Master includes Glimmer and GeneMark for gene calling, we all know how tedious it is to use additional gene calling programs other than those two. To this end, we created Phage Commander, a program that runs a genome through multiple gene calling programs simultaneously. Phage Commander bundles the following programs: Glimmer, GeneMark, host-trained GeneMark.hmm, GeneMark S, GeneMark with Heuristics, GeneMark S2, Prodigal, RAST, MetaGene, and Aragorn. Genes and their coordinates are output to a single spreadsheet for easy visualization; genes are color coded based on how many programs call them. The results can be exported in GenBank formatted files (.gb), for import and further processing in DNA Master. Once in DNA Master, it's as if DNA Master included more gene calling programs than just Glimmer and GeneMark. Phage Commander is super easy to install and use, and runs on Mac, Windows and Linux. It can be downloaded here: https://github.com/sarah-harris/PhageCommander A publication describing Phage Commander has been published in Phage: Therapy, Applications and Research: https://www.liebertpub.com/doi/10.1089/phage.2020.0044 Phage Commander has been used by the SEA-PHAGES class at UNLV and the students and instructors love it. It is very easy to use, but feel free to shoot me an email anyimte if you have any questions or issues. Best, Philippos philippos.tsourkas@unlv.edu ptsourkas@gmail.com Edited 10 Jan, 2022 23:37

Link to this post | posted 10 Jan, 2022 23:24

Hello everyone, I would like to introduce Phage Commander, a new genome annotation tool developed in our lab. Phage Commander is designed to make genome annotation with multiple gene calling programs easier, faster, and less error prone. While DNA Master includes Glimmer and GeneMark for gene calling, we all know how tedious it is to use additional gene calling programs other than those two. To this end, we created Phage Commander, a program that runs a genome through multiple gene calling programs simultaneously. Phage Commander bundles the following programs: Glimmer, GeneMark, host-trained GeneMark.hmm, GeneMark S, GeneMark with Heuristics, GeneMark S2, Prodigal, RAST, MetaGene, and Aragorn. Genes and their coordinates are output to a single spreadsheet for easy visualization; genes are color coded based on how many programs call them. The results can be exported in GenBank formatted files (.gb), for import and further processing in DNA Master. Once in DNA Master, it's as if DNA Master included more gene calling programs than just Glimmer and GeneMark. Phage Commander is super easy to install and use, and runs on Mac, Windows and Linux. It can be downloaded here:
https://github.com/sarah-harris/PhageCommander
A publication describing Phage Commander has been published in Phage: Therapy, Applications and Research:
https://www.liebertpub.com/doi/10.1089/phage.2020.0044

Phage Commander has been used by the SEA-PHAGES class at UNLV and the students and instructors love it. It is very easy to use, but feel free to shoot me an email anyimte if you have any questions or issues.

Best,
Philippos
philippos.tsourkas@unlv.edu
ptsourkas@gmail.com

Edited 10 Jan, 2022 23:37

Link to this post \| posted 12 Jan, 2022 21:04
c.sunnen	Thanks for this! We're already using your 2019 paper, "A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation," in class as an introduction to both annotation and reading the primary literature. Yay! Nikki

Link to this post \| posted 12 Jan, 2022 22:10
ptsourkas	Glad you found it useful. Thanks for sharing!

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New annotation software