VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes

Author:

Hepp Benjamin1,Lorieux Florence1,Degaugue Augustin1,Oberto Jacques1ORCID

Affiliation:

1. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay , 91198 Gif-sur-Yvette cedex, France

Abstract

Abstract Motivation Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing their evolutionary history, monitoring the environment, and creating innovative biotechnologies. However, accessing the necessary data can be challenging due to a lack of dedicated comparative genomic tools and viral and phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have the computational proficiency required to manipulate large amounts of genomic data. Results We have developed VAPEX (Virus And Phage EXplorer), a web server which is supported by a database and features a user-friendly web interface. This tool enables users to easily perform various genomic analysis queries on all natural viruses and phages that have been fully sequenced and are listed in the NCBI compendium. VAPEX therefore excels in producing visual depictions of fully resolved synteny maps, which is one of its key strengths. VAPEX has the ability to exhibit a vast array of orthologous gene classes simultaneously through the use of symbolic representation. Additionally, VAPEX can fully analyze user-submitted viral and phage genomes, including those that have not yet been annotated. Availability and implementation VAPEX can be accessed from all current web browsers such as Chrome, Firefox, Edge, Safari, and Opera. VAPEX is freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/.

Funder

Centre National de la Recherche Scientifique

Agence Nationale de la Recherche

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Reference19 articles.

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