Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Phigaro: high throughput prophage sequence annotation

View ORCID ProfileElizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Vadim M. Govorun
doi: https://doi.org/10.1101/598243
Elizaveta V. Starikova
1Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Elizaveta V. Starikova
  • For correspondence: hed.robin@gmail.com
Polina O. Tikhonova
2Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nikita A. Prianichnikov
1Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chris M. Rands
1Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Evgeny M. Zdobnov
2Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vadim M. Govorun
2Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Summary Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated “prophage genome maps” and marks possible transposon insertion spots inside prophages. It provides putative taxonomic annotations that can distinguish tailed from non-tailed phages. It is applicable for mining prophage regions from large metagenomic datasets.

Availability Source code for Phigaro is freely available for download at https://github.com/bobeobibo/phigaro along with test data. The code is written in Python.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted April 22, 2019.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Phigaro: high throughput prophage sequence annotation
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Phigaro: high throughput prophage sequence annotation
Elizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Vadim M. Govorun
bioRxiv 598243; doi: https://doi.org/10.1101/598243
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Phigaro: high throughput prophage sequence annotation
Elizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Vadim M. Govorun
bioRxiv 598243; doi: https://doi.org/10.1101/598243

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3606)
  • Biochemistry (7575)
  • Bioengineering (5529)
  • Bioinformatics (20806)
  • Biophysics (10333)
  • Cancer Biology (7986)
  • Cell Biology (11644)
  • Clinical Trials (138)
  • Developmental Biology (6610)
  • Ecology (10214)
  • Epidemiology (2065)
  • Evolutionary Biology (13623)
  • Genetics (9543)
  • Genomics (12851)
  • Immunology (7923)
  • Microbiology (19551)
  • Molecular Biology (7666)
  • Neuroscience (42127)
  • Paleontology (308)
  • Pathology (1258)
  • Pharmacology and Toxicology (2203)
  • Physiology (3268)
  • Plant Biology (7044)
  • Scientific Communication and Education (1294)
  • Synthetic Biology (1951)
  • Systems Biology (5427)
  • Zoology (1118)