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Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 9683)

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. The source code is freely available at https://github.com/anzaika/selectoscope.

Keywords

  • Positive selection
  • Codeml
  • Fastcodeml

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Acknowledgements

This study was supported by the Scientific & Technological Cooperation Program Switzerland-Russia (RFBR grant 16-54-21004 and Swiss National Science Foundation project ZLRZ3_163872).

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Correspondence to Andrey V. Zaika .

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Zaika, A.V., Davydov, I.I., Gelfand, M.S. (2016). Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2016. Lecture Notes in Computer Science(), vol 9683. Springer, Cham. https://doi.org/10.1007/978-3-319-38782-6_21

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  • DOI: https://doi.org/10.1007/978-3-319-38782-6_21

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