MIT Libraries homeMIT Libraries logoDSpace@MIT

MIT
View Item 
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

Optimizing a global alignment of protein interaction networks

Author(s)
Ma, C.-Y.; Liao, C.-S.; Berger, Bonnie; Chindelevitch, Leonid
Thumbnail
DownloadChindelevitch_2013-Optimizing global alignment.pdf (273.7Kb)
PUBLISHER_CC

Publisher with Creative Commons License

Creative Commons Attribution

Terms of use
http://creativecommons.org/licenses/by/3.0/
Metadata
Show full item record
Abstract
Motivation: The global alignment of protein interaction networks is a widely studied problem. It is an important first step in understanding the relationship between the proteins in different species and identifying functional orthologs. Furthermore, it can provide useful insights into the species’ evolution. Results: We propose a novel algorithm, PISwap, for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other intractable problems. PISwap can begin with different types of network alignment approaches and then iteratively adjust the initial alignments by incorporating network topology information, trading it off for sequence information. In practice, our algorithm efficiently refines other well-studied alignment techniques with almost no additional time cost. We also show the robustness of the algorithm to noise in protein interaction data. In addition, the flexible nature of this algorithm makes it suitable for different applications of network alignment. This algorithm can yield interesting insights into the evolutionary dynamics of related species. Availability: Our software is freely available for non-commercial purposes from our Web site, http://piswap.csail.mit.edu/.
Date issued
2013-09
URI
http://hdl.handle.net/1721.1/82616
Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Mathematics
Journal
Bioinformatics
Publisher
Oxford University Press
Citation
Chindelevitch, L., C.-Y. Ma, C.-S. Liao, and B. Berger. “Optimizing a global alignment of protein interaction networks.” Bioinformatics 29, no. 21 (October 18, 2013): 2765-2773.
Version: Final published version
ISSN
1367-4803
1460-2059

Collections
  • MIT Open Access Articles

Browse

All of DSpaceCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

My Account

Login

Statistics

OA StatisticsStatistics by CountryStatistics by Department
MIT Libraries homeMIT Libraries logo

Find us on

Twitter Facebook Instagram YouTube RSS

MIT Libraries navigation

SearchHours & locationsBorrow & requestResearch supportAbout us
PrivacyPermissionsAccessibility
MIT
Massachusetts Institute of Technology
Content created by the MIT Libraries, CC BY-NC unless otherwise noted. Notify us about copyright concerns.