NetMatch: a Cytoscape plugin for searching biological networks

被引:46
作者
Ferro, A.
Giugno, R.
Pigola, G.
Pulvirenti, A.
Skripin, D.
Bader, G. D.
Shasha, D.
机构
[1] Univ Catania, Dipartimento Matemat & Informat, I-95125 Catania, Italy
[2] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada
[3] Univ Toronto, Dept Med Genet & Microbiol, Toronto, ON M5S 3E1, Canada
[4] NYU, Courant Inst Math Sci, New York, NY 10012 USA
关键词
D O I
10.1093/bioinformatics/btm032
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
NetMatch is a Cytoscape plugin which allows searching biological networks for subcomponents matching a given query. Queries may be approximate in the sense that certain parts of the subgraph-query may be left unspecified. To make the query creation process easy, a drawing tool is provided. Cytoscape is a bioinformatics software platform for the visualization and analysis of biological networks.
引用
收藏
页码:910 / 912
页数:3
相关论文
共 7 条
[1]   Network biology:: Understanding the cell's functional organization [J].
Barabási, AL ;
Oltvai, ZN .
NATURE REVIEWS GENETICS, 2004, 5 (02) :101-U15
[2]   A (sub)graph isomorphism algorithm for matching large graphs [J].
Cordella, LP ;
Foggia, P ;
Sansone, C ;
Vento, M .
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2004, 26 (10) :1367-1372
[3]   Network motifs: Simple building blocks of complex networks [J].
Milo, R ;
Shen-Orr, S ;
Itzkovitz, S ;
Kashtan, N ;
Chklovskii, D ;
Alon, U .
SCIENCE, 2002, 298 (5594) :824-827
[4]   MAVisto:: a tool for the exploration of network motifs [J].
Schreiber, F ;
Schwöbbermeyer, H .
BIOINFORMATICS, 2005, 21 (17) :3572-3574
[5]   Cytoscape: A software environment for integrated models of biomolecular interaction networks [J].
Shannon, P ;
Markiel, A ;
Ozier, O ;
Baliga, NS ;
Wang, JT ;
Ramage, D ;
Amin, N ;
Schwikowski, B ;
Ideker, T .
GENOME RESEARCH, 2003, 13 (11) :2498-2504
[6]   FANMOD: a tool for fast network motif detection [J].
Wernicke, S ;
Rasche, F .
BIOINFORMATICS, 2006, 22 (09) :1152-1153
[7]   The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks [J].
Yip, Kevin Y. ;
Yu, Haiyuan ;
Kim, Philip M. ;
Schultz, Martin ;
Gerstein, Mark .
BIOINFORMATICS, 2006, 22 (23) :2968-2970