Development of a novel clustering tool for linear peptide sequences

Immunology
Sandeep Kumar DhandaAlessandro Sette

Abstract

Epitopes identified in large-scale screens of overlapping peptides often share significant levels of sequence identity, complicating the analysis of epitope-related data. Clustering algorithms are often used to facilitate these analyses, but available methods are generally insufficient in their capacity to define biologically meaningful epitope clusters in the context of the immune response. To fulfil this need we developed an algorithm that generates epitope clusters based on representative or consensus sequences. This tool allows the user to cluster peptide sequences on the basis of a specified level of identity by selecting among three different method options. These include the 'clique method', in which all members of the cluster must share the same minimal level of identity with each other, and the 'connected graph method', in which all members of a cluster must share a defined level of identity with at least one other member of the cluster. In cases where it is not possible to define a clear consensus sequence with the connected graph method, a third option provides a novel 'cluster-breaking algorithm' for consensus sequence driven sub-clustering. Herein we demonstrate the tool's clustering performance and applicability u...Continue Reading

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Citations

May 23, 2019·Nucleic Acids Research·Sandeep Kumar DhandaBjoern Peters
Feb 12, 2020·Annual Review of Immunology·Bjoern PetersAlessandro Sette
Oct 12, 2019·BMC Bioinformatics·Swapnil MahajanBjoern Peters
Apr 24, 2020·Journal of Immunology Research·Ricardo da Silva AntunesAlessandro Sette
Nov 26, 2019·Immunogenetics·Sheridan MartiniAlessandro Sette
Nov 18, 2020·Viruses·Jose MateusDaniela Weiskopf
Jan 20, 2021·Computers in Biology and Medicine·Anjali LathwalGajendra P S Raghava
Mar 9, 2021·Frontiers in Immunology·Jessica Badolato-CorrêaLuzia Maria de-Oliveira-Pinto
Oct 24, 2020·Cell·Benjamin J MeckiffPandurangan Vijayanand
Jul 9, 2021·Cell Host & Microbe·Alba GrifoniAlessandro Sette
Oct 7, 2021·Human Vaccines & Immunotherapeutics·Maria da Conceição Viana InvençãoAntonio Carlos de Freitas

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Methods Mentioned

BETA
Assay

Software Mentioned

PepServe
Hammock
django
Python scripts
GibbsCluster
UCLUST
javascripts
networkx
cluster2
megapool

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