Phigaro: high-throughput prophage sequence annotation

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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 is applicable for mining prophage regions from large metagenomic datasets.

Availability and implementation

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.

Supplementary information

Supplementary data are available at Bioinformatics online.

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Most cited references 16

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Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt, Gwo-Liang Chen, Philip LoCascio … (2010)

Background The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. Results With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. Conclusion We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.

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PHASTER: a better, faster version of the PHAST phage search tool

David L. Arndt, Jason Grant, Ana Marcu … (2016)

PHASTER (PHAge Search Tool – Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST, while the addition of 80 CPUs to the PHASTER compute cluster are responsible for the remaining speed-up. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file. A number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of PHASTER's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER's web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. PHASTER is available online at www.phaster.ca.

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HMMER web server: 2018 update

Simon C Potter, Aurélien Luciani, Sean R. Eddy … (2018)

Abstract The HMMER webserver [http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the HMMER software suite (http://hmmer.org). The results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) which has been expanded in scope, such that all result presentations are available via both HTML and API. Furthermore, we have refactored our JavaScript visualization library to provide standalone components for different result representations. These consume the aforementioned API and can be integrated into third-party websites. The range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile HMM library (6 in total). To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.

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Author and article information

Contributors

Elizaveta V Starikova: (View ORCID Profile)

Journal

Title: Bioinformatics

Publisher: Oxford University Press (OUP)

ISSN (Print): 1367-4803

ISSN (Electronic): 1460-2059

Publication date Created: June 15 2020

Publication date Created: June 01 2020

Publication date Created: April 20 2020

Publication date Other: June 15 2020

Publication date (Print): June 01 2020

Publication date (Electronic): April 20 2020

Volume: 36

Issue: 12

Pages: 3882-3884

Affiliations

[1 ]Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia

[2 ]Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva 1206, Switzerland

Article

DOI: 10.1093/bioinformatics/btaa250

PubMed ID: 32311023

SO-VID: a5412f57-3efa-43e4-ad53-bb44993af4fb

License:

https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

Phigaro: high-throughput prophage sequence annotation

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Abstract

Summary

Availability and implementation

Supplementary information

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Network and Systems Medicine

Most cited references 16

Prodigal: prokaryotic gene recognition and translation initiation site identification

PHASTER: a better, faster version of the PHAST phage search tool

HMMER web server: 2018 update

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