University of Surrey

Test tubes in the lab Research in the ATI Dance Research

BRepertoire: A user-friendly web server for analysing antibody repertoire data

Margreitter, Christian, Lu, Hui-Chun, Townsend, Catherine, Stewart, Alexander, Dunn-Walters, Deborah and Fraternali, Franca (2018) BRepertoire: A user-friendly web server for analysing antibody repertoire data Nucleic Acids Research.

[img]
Preview
Text
BRepertoire.pdf - Version of Record
Available under License Creative Commons Attribution.

Download (1MB) | Preview

Abstract

Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication.We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server’s functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Biosciences and Medicine
Authors :
NameEmailORCID
Margreitter, Christian
Lu, Hui-Chun
Townsend, Catherine
Stewart, Alexanderalexander.stewart@surrey.ac.uk
Dunn-Walters, Deborahd.dunn-walters@surrey.ac.uk
Fraternali, Franca
Date : 2018
Funders : Medical Research Council (MRC), Biotechnology and Biological Sciences Research Council (BBSRC)
Identification Number : 10.1093/nar/gky276
Grant Title : Immunology of the Lifecourse programme grant: MABRA ‘Multiscale analysis of B cell responses in ageing’
Copyright Disclaimer : © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Related URLs :
Additional Information : Supplementary Data are available at NAR Online. (See 'related URLs' dataset link.)
Depositing User : Clive Harris
Date Deposited : 13 Apr 2018 10:14
Last Modified : 13 Apr 2018 11:46
URI: http://epubs.surrey.ac.uk/id/eprint/846218

Actions (login required)

View Item View Item

Downloads

Downloads per month over past year


Information about this web site

© The University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom.
+44 (0)1483 300800