Fast and accurate alignment of multiple protein networks

Maxim Kalaev, Vineet Bafna, Roded Sharan

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

Abstract

Comparative analysis of protein networks has proven to be a powerful approach for elucidating network structure and predicting protein function and interaction. A fundamental challenge for the successful application of this approach is to devise an efficient multiple network alignment algorithm. Here we present a novel framework for the problem. At the heart of the framework is a novel representation of multiple networks that is only linear in their size as opposed to current exponential representations. Our alignment algorithm is very efficient, being capable of aligning 10 networks with tens of thousands of proteins each in minutes. We show that our algorithm outperforms a previous strategy for the problem that is based on progressive alignment, and produces results that are more in line with current biological knowledge.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 12th Annual International Conference, RECOMB 2008, Proceedings
Pages246-256
Number of pages11
DOIs
StatePublished - 2008
Event"12th Annual InternationalConference on REsearch in COmputational Molecular Biology, RECOMB 2008" - Singapore, Singapore
Duration: 30 Mar 20082 Apr 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4955 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference"12th Annual InternationalConference on REsearch in COmputational Molecular Biology, RECOMB 2008"
Country/TerritorySingapore
CitySingapore
Period30/03/082/04/08

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