Selectoscope: A modern web-app for positive selection analysis of genomic data

Andrey V. Zaika, Iakov I. Davydov, Mikhail S. Gelfand

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Selectoscope is a web application which combines a number of popular tools used to infer positive selection in an easy to use pipeline. A set of homologous DNA sequences to be analyzed and evaluated are submitted to the server by uploading protein-coding gene sequences in the FASTA format. The sequences are aligned and a phylogenetic tree is constructed. The codeml procedure from the PAML package is used first to adjust branch lengths and to find a starting point for the likelihood maximization, then FastCodeML is executed. Upon completion, branches and positions under positive selection are visualized simultaneously on the tree and alignment viewers. Run logs are accessible through the web interface. Selectoscope is based on the Docker virtualization technology. This makes the application easy to install with a negligible performance overhead. The application is highly scalable and can be used on a single PC or on a large high performance clusters.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 12th International Symposium, ISBRA 2016, Proceedings
EditorsAnu Bourgeois, Pavel Skums, Xiang Wan, Alex Zelikovsky
PublisherSpringer Verlag
Pages253-257
Number of pages5
ISBN (Print)9783319387819
DOIs
Publication statusPublished - 2016
Externally publishedYes
Event12th International Symposium on Bioinformatics Research and Applications, ISBRA 2016 - Minsk, Belarus
Duration: 5 Jun 20168 Jun 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9683
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference12th International Symposium on Bioinformatics Research and Applications, ISBRA 2016
Country/TerritoryBelarus
CityMinsk
Period5/06/168/06/16

Keywords

  • Codeml
  • Fastcodeml
  • Positive selection

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