Tag: Virus

VirusFinder 2.0 – Detect Viruses and their Integration Sites in Host Genomes

VirusFinder 2.0

:: DESCRIPTION

VirusFinder is a new software tool for characterizing intra-host viruses through next generation sequencing (NGS) data.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Java
  • Perl

:: DOWNLOAD

  VirusFinder

:: MORE INFORMATION

Citation:

PLoS One. 2013 May 24;8(5):e64465. doi: 10.1371/journal.pone.0064465. Print 2013.
VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data.
Wang Q1, Jia P, Zhao Z.

VirusScan 1.1 – Detect Virus from Next Generation Sequencing data

VirusScan 1.1

:: DESCRIPTION

VirusScan pipeline is a fully automated and modular software package designed for the fast and accurate detection of known viruses from NGS data.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

VirusScan

:: MORE INFORMATION

Citation

Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R 3rd, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L.
Divergent viral presentation among human tumors and adjacent normal tissues.
Sci Rep. 2016 Jun 24;6:28294. doi: 10.1038/srep28294. PMID: 27339696; PMCID: PMC4919655.

DeNovo – Virus-Host Sequence-Based Protein-Protein Interaction Prediction

DeNovo

:: DESCRIPTION

DeNovo is a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins.

::DEVELOPER

DeNovo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • MatLab

:: DOWNLOAD

 DeNovo

:: MORE INFORMATION

Citation

DeNovo: Virus-Host Sequence-Based Protein-Protein Interaction Prediction.
Eid FE, ElHefnawi M, Heath LS.
Bioinformatics. 2015 Dec 16. pii: btv737.

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.

VirusSeeker – Virus Discovery and Virome Composition Analysis

VirusSeeker

:: DESCRIPTION

VirusSeeker is a set of fully automated and modular software package designed for mining next generation sequencing data form Illumina platform to identify sequences of viral origin.

::DEVELOPER

The Zhao Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

VirusSeeker

:: MORE INFORMATION

Citation:

Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D.
VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.
Virology. 2017 Mar;503:21-30. doi: 10.1016/j.virol.2017.01.005. Epub 2017 Jan 18. PMID: 28110145; PMCID: PMC5326578.

PhEVER 2.0 – Viral Evolution and Virus/host Co-evolution

PhEVER 2.0

:: DESCRIPTION

PhEVER (Phylogenetic Exploration of Viruses’ Evolutionary Relationships) is a database of homologous gene families providing information for the understanding of virus/host co-evolution. Each family supplies pre-computed alignment and phylogeny.

::DEVELOPER

PhEVER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Jan;39(Database issue):D569-75. doi: 10.1093/nar/gkq1013.
PhEVER: a database for the global exploration of virus-host evolutionary relationships.
Palmeira L, Penel S, Lotteau V, Rabourdin-Combe C, Gautier C.

IVA 1.0.9 – Iterative Virus Assembler

IVA 1.0.9

:: DESCRIPTION

IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 IVA

:: MORE INFORMATION

Citation

IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Feb 28. pii: btv120.

PrimerHunter 1.0.2 – Primer Design for PCR-Based Virus Subtype Identification

PrimerHunter 1.0.2

:: DESCRIPTION

PrimerHunter is a tool for selecting highly sensitive and specific primers for virus subtyping. It takes as input sets of both target and non-target sequences and ensures that selected primers amplify all target sequences and none of the non-target sequences by relying on accurate melting temperature computations based on the nearest-neighbor model of Santalucia and the fractional programming algorithm of  Leber et al.

PrimerHunter Online version

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PrimerHunter

:: MORE INFORMATION

Citation:

J. Duitama and D.M. Kumar and E. Hemphill and M. Khan and I.I. Mandoiu and C.E. Nelson,
PrimerHunter: A Primer Design Tool for PCR-Based Virus Subtype Identification,
Nucleic Acids Research 37, pp. 2483-2492, 2009