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Nucleic Acids Research Advance Access originally published online on June 2, 2009
Nucleic Acids Research 2009 37(Web Server issue):W106-W108; doi:10.1093/nar/gkp474
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W106-W108
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

Torque: topology-free querying of protein interaction networks

Sharon Bruckner1,*, Falk Hüffner1, Richard M. Karp2, Ron Shamir1 and Roded Sharan1,*

1The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA

*To whom correspondence should be addressed. Tel: +972 3 640 7139; Fax: +972 3 640 9357; Email: bruckner{at}tau.ac.il Correspondence may also be addressed to Roded Sharan. Email: roded{at}tau.ac.il

Received January 27, 2009. Revised April 24, 2009. Accepted May 17, 2009.

TORQUE is a tool for cross-species querying of protein–protein interaction networks. It aims to answer the following question: given a set of proteins constituting a known complex or a pathway in one species, can a similar complex or pathway be found in the protein network of another species? To this end, TORQUE seeks a matching set of proteins that are sequence similar to the query proteins and span a connected region of the target network, while allowing for both insertions and deletions. Unlike existing approaches, TORQUE does not require knowledge of the interconnections among the query proteins. It can handle large queries of up to 25 proteins. The TORQUE web server is freely available for use at http://www.cs.tau.ac.il/~bnet/torque.html.


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