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

Détails

Ressource 1Télécharger: Seletescopepostprint.pdf (1766.71 [Ko])
Etat: Serval
Version: de l'auteur
ID Serval
serval:BIB_AA1D1FFA391C
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data
Périodique
Bioinformatics Research and Applications
Auteur(s)
Zaika A.V., Davydov I.I., Gelfand M.S.
ISBN
978-3-319-38781-9
978-3-319-38782-6
ISSN
1611-3349
ISSN-L
0302-9743
Statut éditorial
Publié
Date de publication
2016
Peer-reviewed
Oui
Volume
9683
Pages
253-257
Langue
anglais
Résumé
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.
Mots-clé
Positive selection, Codeml, Fastcodeml
Web of science
Création de la notice
07/02/2017 10:31
Dernière modification de la notice
03/03/2018 20:23
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