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
    Barabási, AL
    Oltvai, ZN
    [J]. NATURE REVIEWS GENETICS, 2004, 5 (02) : 101 - U15
  • [2] A (sub)graph isomorphism algorithm for matching large graphs
    Cordella, LP
    Foggia, P
    Sansone, C
    Vento, M
    [J]. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2004, 26 (10) : 1367 - 1372
  • [3] Network motifs: Simple building blocks of complex networks
    Milo, R
    Shen-Orr, S
    Itzkovitz, S
    Kashtan, N
    Chklovskii, D
    Alon, U
    [J]. SCIENCE, 2002, 298 (5594) : 824 - 827
  • [4] MAVisto:: a tool for the exploration of network motifs
    Schreiber, F
    Schwöbbermeyer, H
    [J]. BIOINFORMATICS, 2005, 21 (17) : 3572 - 3574
  • [5] Cytoscape: A software environment for integrated models of biomolecular interaction networks
    Shannon, P
    Markiel, A
    Ozier, O
    Baliga, NS
    Wang, JT
    Ramage, D
    Amin, N
    Schwikowski, B
    Ideker, T
    [J]. GENOME RESEARCH, 2003, 13 (11) : 2498 - 2504
  • [6] FANMOD: a tool for fast network motif detection
    Wernicke, S
    Rasche, F
    [J]. BIOINFORMATICS, 2006, 22 (09) : 1152 - 1153
  • [7] The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
    Yip, Kevin Y.
    Yu, Haiyuan
    Kim, Philip M.
    Schultz, Martin
    Gerstein, Mark
    [J]. BIOINFORMATICS, 2006, 22 (23) : 2968 - 2970