Phigaro v2.3.0 – Predicting Phages and Prophages

Phigaro v2.3.0

:: DESCRIPTION

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.

::DEVELOPER

Prof Zdobnov Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Phigaro

:: MORE INFORMATION

Citation

Starikova EV, Tikhonova PO, Prianichnikov NA, Rands CM, Zdobnov EM, Ilina EN, Govorun VM.
Phigaro: high-throughput prophage sequence annotation.
Bioinformatics. 2020 Jun 1;36(12):3882-3884. doi: 10.1093/bioinformatics/btaa250. PMID: 32311023.

MetaGeneAnnotator – Gene Finding program for Prokaryote and Phage

MetaGeneAnnotator

:: DESCRIPTION

MetaGeneAnnotator is a prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.

::DEVELOPER

Hideki Noguchi (hnoguchi @nig.ac.jp)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

MetaGeneAnnotator

:: MORE INFORMATION

Citation

MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes.
Noguchi H, Taniguchi T, Itoh T.
DNA Res. 2008 Dec;15(6):387-96. doi: 10.1093/dnares/dsn027.

FastViromeExplorer – Virus and Phage Identification and Abundance profiling in Metagenomics data

FastViromeExplorer

:: DESCRIPTION

FastViromeExplorer is a stand-alone pipeline for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

FastViromeExplorer

:: MORE INFORMATION

Citation

Tithi SS, Aylward FO, Jensen RV, Zhang L.
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.
PeerJ. 2018 Jan 12;6:e4227. doi: 10.7717/peerj.4227. PMID: 29340239; PMCID: PMC5768174.

PHAST 20161213 / PHASTER – Fast Phage Search tool

PHAST 20161213 / PHASTER

:: DESCRIPTION

PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.

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,.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

PHASTER: a better, faster version of the PHAST phage search tool.
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS.
Nucleic Acids Res. 2016 May 3. pii: gkw387.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W347-52. doi: 10.1093/nar/gkr485. Epub 2011 Jun 14.
PHAST: a fast phage search tool.
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS.

PhiSiGns 1.2 – Indentify Signature Genes in Phages and Design Primers

PhiSiGns 1.2

:: DESCRIPTION

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples. PhiSiGns is intended for phage biologists who want to find common conserved genes in phages for evolution or phylogeny based studies, or who are interested in designing primers that can be used to explore environmental phage diversity.

PhiSiGns Online Version

::DEVELOPER

the Breitbart lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhiSiGns

:: MORE INFORMATION

Citation:

Bhakti Dwivedi, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards, and Mya Breitbart (in review)
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.
BMC Bioinformatics 2012, 13:37

PHYPred – Identifying Phage Enzymes and Hydrolases

PHYPred

:: DESCRIPTION

The web-server PHYPred was developed to identify the phage enzymes and hydrolases based on the sequence information.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PHYPred: a tool for identifying bacteriophage enzymes and hydrolases.
Ding H, Yang W, Tang H, Feng PM, Huang J, Chen W, Lin H.
Virol Sin. 2016 Aug;31(4):350-2. doi: 10.1007/s12250-016-3740-6.

PVPred – Identification of Phage Virion Proteins

PVPred

:: DESCRIPTION

PVPred is a sequence-based tool for identifying phage virion proteins

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Biosyst. 2014 Jun 16. [Epub ahead of print]
Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis.
Ding H1, Feng PM, Chen W, Lin H.

WIsH 1.0 – Prediction of Prokaryotic Hosts of Phages from Genomic Sequences

WIsH 1.0

:: DESCRIPTION

WIsH(Who Is the Host) can identify bacterial hosts from metagenomic data, keeping good accuracy even on smaller contigs.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • C Compiler
:: DOWNLOAD

WIsH

:: MORE INFORMATION

Citation:

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs.
Galiez C, Siebert M, Enault F, Vincent J, Söding J.
Bioinformatics. 2017 Oct 1;33(19):3113-3114. doi: 10.1093/bioinformatics/btx383.