PHANOTATE: Gene finding in phages

Issue 120 | April 2, 2021

7 min read

For the 2nd webinar of the Phage Bioinformatics Webinar Series jointly organized by IBRC and Phage Directory, we hosted Katelyn McNair, a research scholar at the University of California, Irvine and San Diego State University. This week, we bring you a recap of her talk (written by Dr. Rohit Kongari) and the recording!

What’s New

Fixed Phage, a Glasgow-based phage biotech company commercialising phage immobilisation and stabilisation-based technology, has secured £2.4 million to scale up its fight against new microbial threats that pose risks to human health and agriculture.

PBD Biotech has secured a £2.3m investment to take Actiphage®, a rapid, accurate phage-based bovine TB test through to validation by the World Organisation for Animal Health. This test has potential to enable farmers to effectively remove TB from their herds.

James Doub (University of Maryland School of Medicine) and colleagues published a new paper in Pharmaceuticals on their successful treatment of a recalcitrant Staphylococcus epidermidis prosthetic knee infection with intraoperative phage therapy. The phage used in this case is the first ɛ2 phage (‘bred’ phages generated at PhagoMed by superinfecting S. epidermidis strains with multiple wild type phages) to be used in vivo.

Eleanor Townsend (University of Warwick) and colleagues published a new paper in PHAGE describing the isolation and characterization of 30 novel, genetically diverse Klebsiella phages.

The Center for Phage Technology has published CPT-GFFParser, an extensively featured Python parser for GFF format reading/writing developed by the CPT bioinformatics team (main author Anthony Criscione). It’s now available as a python package here.

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The Bordenstein Lab (Vanderbilt University, Nashville, Tennessee) is recruiting at all levels to join projects on the molecular mechanisms and evolution of (i) phage WO genes that cause symbiotic phenotypes and (ii) insect genes that regulate maternal inheritance of symbionts (Wolbachia). The projects explore proteins that hijack host cells, genomes, and animal reproduction, as well as insect genes that suppress inherited symbiont densities. Contact Dr. Bordenstein at [email protected] with informal inquires or a pdf package.

Sensei Biotherapeutics is seeking a Scientist to help create better immunotherapeutics by investigating mechanisms of cross-presentation of phage lambda-displayed antigens to optimize cancer immunotherapy.

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Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

Join us April 13 at 4PM CEST for PHAVES #14, which will be a seminar with Dr. Clara Torres-Barceló (Plant Pathology Unit, INRAE, Avignon, France) entitled: “Jack of all strains, master of none? Host range and efficacy in phages of a phytopathogenic bacterium”. Small group networking to follow! Register here!

We’re excited to announce that we’re starting a new stream of PHAVES, running parallel to our researcher-focused series. The new series will focus on phage therapy in the clinic. We’ll be featuring clinicians who have treated patients with phages, but will also bring in patients and beyond. The goal is to facilitate knowledge exchange between those using phages and those interested in learning more.

To start us off, join us April 14 at 3pm Pacific time for an interview with Dr. Randy Fish (DPM, Podiatrist in chronic wound healing and clinical research using bacteriophage in diabetic foot infections, Tacoma Diabetic Foot Clinic and PhageBiotics Research Foundation).

At this event, Jessica will interview Randy about his work and vision when it comes to using phages to treat diabetic foot infections. We’ll discuss Randy’s goals to look at topical or localized use of phage to avoid the use of antibiotics, his vision on using phage to catch infections early, and his interest in testing how much and how often phage should be applied for optimal results. Small group networking to follow! Register here!

Missed last week’s Phage Phriday on Clubhouse? Here’s the recording of the Q&A with Dr. Steffanie Strathdee, author of “The Perfect Predator”.

Want more Clubhouse? Get the app (iphone only) and follow Phage Club — currently running weekly events Wednesday nights at 9PM Eastern and Friday afternoons at 1PM Central.

PHANOTATE: Gene finding in phages

Postdoctoral Researcher

Stibitz Lab, FDA

Skills

Bioinformatics, Biotechnology, Molecular Biology, Phage isolation, Phage Therapy, Phage-host interactions, Teaching, Phage Genomics, RNA Sequencing

I am a Phage Biologist at heart with a strong technical background in Biochemistry, Bioinformatics, Phage Genomics, Microbiology and Molecular Biology. I worked on the role of phage spanins in host lysis for my PhD under the guidance of Dr. Ryland Young at Texas A&M University. I am currently working on understanding the host-phage interactions between Staphylococcus aureus and phage K towards use in phage therapy applications.

Phage Hosts

Enterobacter

Enterococcus

Staphylococcus aureus

For the 2nd webinar of the Phage Bioinformatics Lecture Series being jointly organized by IBRC and Phage Directory, we hosted Katelyn McNair, a research scholar at the University of California, Irvine and San Diego State University, USA. Check out this recap of her talk!

Phage genome annotation: the right way and/or the easy way!

YouTube video

Highlights of Katelyn’s talk

Katelyn started off by comparing bacterial and phage genome organizations and contrasting existing tools for gene finding like Glimmer and Genemark to PHANOTATE, the phage genome annotation software she developed.
She then explained the algorithm behind gene finding programs and how the presence of completely/partially overlapping genes in phage genomes can complicate predictions. Therefore it is important that even after running phage genomes through automated annotation software, manual annotation needs to be done to remove false positives or add false negatives.
She demonstrated how to install and run PHANOTATE on an example genome to produce an automated phage gene annotation output and then use the GC frame plot to manually make changes using Artemis.
PHANOTATE is available as an open-source python based tool on Github as well as a part of a fully automated annotation pipeline on the PATRIC website.
She also briefly explained a tool called “Circulaline” that aligns circular genomes based on a common feature that can help identify the proper origin and realign to the correct orientation.

Additional resources

Katelyn’s paper describing PHANOTATE, the first gene finder specifically designed for phage genome annotation
Katelyn’s previous tool, PHACTS, which computationally predicts whether a phage is temperate or virulent

Want more phage bioinformatics? Join our Slack Community, and check out our new page!

As a companion to this series, we’ve launched a Slack channel called #phage-bioinformatics within the Phage Directory Slack. In our community, you can share your questions and work through issues together with the community.

We also created a Phage Bioinformatics resources page, where you’ll find the PDFs, slideshows, links, resources, video recordings etc. collected throughout our webinars and Slack conversations.

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Postdoctoral Researcher

Stibitz Lab, FDA

Skills

Bioinformatics, Biotechnology, Molecular Biology, Phage isolation, Phage Therapy, Phage-host interactions, Teaching, Phage Genomics, RNA Sequencing

Phage Hosts

Enterobacter

Enterococcus

Staphylococcus aureus

How to Cite

To cite this, please use:

Kongari, R. (2021). PHANOTATE: Gene finding in phages. Capsid & Tail, (120). Retrieved from https://phage.directory/capsid/bioinformatics-recap-katelyn-mcnair

BibTeX citation:

@article{bioinformatics-recap-katelyn-mcnair2021,

journal = {Capsid & Tail},
number = {120},
publisher = {Phage Directory},
title = {PHANOTATE: Gene finding in phages},
url = {https://phage.directory/capsid/bioinformatics-recap-katelyn-mcnair},
author = {Kongari, Rohit},
date = {2021-04-02},
year = {2021},
month = {4},
day = {2},

}

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