Literature DB >> 25428870

Unraveling the web of viroinformatics: computational tools and databases in virus research.

Deepak Sharma1, Pragya Priyadarshini2, Sudhanshu Vrati2.   

Abstract

The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain--viroinformatics. The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic fever virus [HFV], human papillomavirus [HPV], West Nile virus, etc.) as well as distinct applications (comparative/diversity analysis, viral recombination, small interfering RNA [siRNA]/short hairpin RNA [shRNA]/microRNA [miRNA] studies, RNA folding, protein-protein interaction, structural analysis, and phylotyping and genotyping) will definitely aid the development of effective drugs and vaccines. However, information about their access and utility is not available at any single source or on any single platform. Therefore, a compendium of various computational tools and resources dedicated specifically to virology is presented in this article.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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Year:  2014        PMID: 25428870      PMCID: PMC4300767          DOI: 10.1128/JVI.02027-14

Source DB:  PubMed          Journal:  J Virol        ISSN: 0022-538X            Impact factor:   5.103


  115 in total

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2.  HERVd: database of human endogenous retroviruses.

Authors:  Jan Paces; Adam Pavlícek; Václav Paces
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells.

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Journal:  Biopolymers       Date:  2007-02-15       Impact factor: 2.505

4.  The influenza virus resource at the National Center for Biotechnology Information.

Authors:  Yiming Bao; Pavel Bolotov; Dmitry Dernovoy; Boris Kiryutin; Leonid Zaslavsky; Tatiana Tatusova; Jim Ostell; David Lipman
Journal:  J Virol       Date:  2007-10-17       Impact factor: 5.103

5.  Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.

Authors:  Allison K Delong; Mingham Wu; Diane Bennett; Neil Parkin; Zhijin Wu; Joseph W Hogan; Rami Kantor
Journal:  AIDS Res Hum Retroviruses       Date:  2011-10-26       Impact factor: 2.205

6.  Viral genome analysis and knowledge management.

Authors:  Carla Kuiken; Hyejin Yoon; Werner Abfalterer; Brian Gaschen; Chienchi Lo; Bette Korber
Journal:  Methods Mol Biol       Date:  2013

7.  FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology.

Authors:  Lars Rønn Olsen; Guang Lan Zhang; Ellis L Reinherz; Vladimir Brusic
Journal:  Immunome Res       Date:  2011

8.  HBVdb: a knowledge database for Hepatitis B Virus.

Authors:  Juliette Hayer; Fanny Jadeau; Gilbert Deléage; Alan Kay; Fabien Zoulim; Christophe Combet
Journal:  Nucleic Acids Res       Date:  2012-11-03       Impact factor: 16.971

9.  HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

Authors:  Li Yin; Jiqiang Yao; Brent P Gardner; Kaifen Chang; Fahong Yu; Maureen M Goodenow
Journal:  Bioinformation       Date:  2012-04-30

10.  PrimerHunter: a primer design tool for PCR-based virus subtype identification.

Authors:  Jorge Duitama; Dipu Mohan Kumar; Edward Hemphill; Mazhar Khan; Ion I Mandoiu; Craig E Nelson
Journal:  Nucleic Acids Res       Date:  2009-03-05       Impact factor: 16.971

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  28 in total

Review 1.  Next-generation sequencing in clinical virology: Discovery of new viruses.

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Review 2.  The Promise of Proteomics in the Study of Oncogenic Viruses.

Authors:  Alison A McBride
Journal:  Mol Cell Proteomics       Date:  2017-01-19       Impact factor: 5.911

Review 3.  Studying the Exposome to Understand the Environmental Determinants of Complex Liver Diseases.

Authors:  Angela C Cheung; Douglas I Walker; Brian D Juran; Gary W Miller; Konstantinos N Lazaridis
Journal:  Hepatology       Date:  2019-12-24       Impact factor: 17.425

4.  CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data.

Authors:  Andrew Routh; Max W Chang; Jason F Okulicz; John E Johnson; Bruce E Torbett
Journal:  Methods       Date:  2015-09-25       Impact factor: 3.608

Review 5.  Variability in Humoral Immunity to Measles Vaccine: New Developments.

Authors:  Iana H Haralambieva; Richard B Kennedy; Inna G Ovsyannikova; Jennifer A Whitaker; Gregory A Poland
Journal:  Trends Mol Med       Date:  2015-11-18       Impact factor: 11.951

Review 6.  Big Data Offers Novel Insights for Oncolytic Virus Immunotherapy.

Authors:  Stephanie L Swift; David F Stojdl
Journal:  Viruses       Date:  2016-02-05       Impact factor: 5.048

Review 7.  Compounds with anti-influenza activity: present and future of strategies for the optimal treatment and management of influenza. Part II: Future compounds against influenza virus.

Authors:  R Gasparini; D Amicizia; P L Lai; N L Bragazzi; D Panatto
Journal:  J Prev Med Hyg       Date:  2014-12

8.  viruSITE-integrated database for viral genomics.

Authors:  Matej Stano; Gabor Beke; Lubos Klucar
Journal:  Database (Oxford)       Date:  2016-12-26       Impact factor: 3.451

Review 9.  Assessing Species Diversity Using Metavirome Data: Methods and Challenges.

Authors:  Damayanthi Herath; Duleepa Jayasundara; David Ackland; Isaam Saeed; Sen-Lin Tang; Saman Halgamuge
Journal:  Comput Struct Biotechnol J       Date:  2017-09-21       Impact factor: 7.271

10.  ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences.

Authors:  Fwu-Shan Shieh; Patrick Jongeneel; Jamin D Steffen; Selena Lin; Surbhi Jain; Wei Song; Ying-Hsiu Su
Journal:  PLoS One       Date:  2017-08-22       Impact factor: 3.240

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