GRAPES: A Software for Parallel Searching on Biological Graphs Targeting Multi-Core Architectures

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Giugno, Rosalba ^a   Bonnici, Vincenzo ^b   Bombieri, Nicola ^b   Pulvirenti, Alfredo ^a   Ferro, Alfredo ^a   Shasha, Dennis ^c  

^a UNIVERSITY OF CATANIA   (Italy)

^b UNIVERSITY OF VERONA   (Italy)

^c NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DATA BASE; DATA MINING; INFORMATION RETRIEVAL; INFORMATION STORAGE; PARALLEL SEARCH ALGORITHM; BIOLOGICAL MODEL; FACTUAL DATABASE;

ANTIVIRUS AGENT;

ANTIVIRAL AGENTS; DATABASES, FACTUAL; MODELS, BIOLOGICAL; SOFTWARE;

EID: 84886012840     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0076911     Document Type: Article

References (30)

1. Kelley B, Sharan R, Karp R, Sittler T, Root D, et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PNAS 100: 11394-11399.
2. Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, et al. (2007) Netmatch: a cytoscape plugin for searching biological networks. Bioinformatics 23: 910-912.
3. Banks E, Nabieva E, Peterson R, Singh M, (2008) Netgrep: fast network schema searches in interactomes. Genome biology 9: R138.
4. Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, et al. (2008) Qnet: A tool for querying protein interaction networks. Computational Biology 15: 913-925.
5. Lacroix V, Fernandes C, Sagot M, (2006) Motif search in graphs: application to metabolic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3: 360-368.
6. Daylight chemical information systems, available: http://www.daylight.com/, accessed 2013 marc 10.
7. Rajapakse H, (2007) Small molecule inhibitors of the xiap protein-protein interaction. Curr Top Med Chem 7: 966-71.
8. Levy D, Pereira-Leal D, Chothia C, Teichmann S, (2006) 3d complex: A structural classification of protein complexes. PLOS Computational Biology 2: e155.
9. Messmer BT, Bunke H, (1995) Subgraph isomorphism detection in polynominal time on preprocessed model graphs. Recent Developments in Computer Vision,Lecture Notes in Computer Science 1035: 373-382.
10. Cordella L, Foggia P, Sansone C, Vento M, (2004) A (sub)graph isomorphism algorithm for matching large graphs. IEEE Transactions on Pattern Analysis and Machine Intelligence 26: 1367-1372.
11. Ullmann JR, (2011) Bit-vector algorithms for binary constraint satisfaction and subgraph isomorphism. Journal of Experimental Algorithmics 15: 1.1-1.64.
12. He H, Singh AK (2006) Closure-tree: An index structure for graph queries. In: Proceedings of the 22nd International Conference on Data Engineering. ICDE'06, p. 38.
13. Zou L, Chen L, Yu J, Lu Y (2008) A novel spectral coding in a large graph database. In: Proceedings of the 11th international conference on Extending database technology: Advances in database technology. ACM, 181-192.
14. Shasha D, Wang JL, Giugno R (2002) Algorithmics and applications of tree and graph searching. Proceeding of the ACM Symposium on Principles of Database Systems (PODS): 39-52.
15. Di Natale R, Ferro A, Giugno R, Mongiovì M, Pulvirenti A, et al. (2010) Sing: Subgraph search in non-homogeneous graphs. BMC Bioinformatics 11: 96.
16. Bonnici V, Ferro A, Giugno R, Pulvirenti A, Shasha D (2010) Enhancing graph database indexing by suffix tree structure. In: Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics. PRIB'10, 195-203.
17. Zhang S, Hu M, Yang J (2007) Treepi: A novel graph indexing method. In: Proceedings of IEEE 23rd International Conference on Data Engineering. ICDE'07, 181-192.
18. Cheng J, Ke Y, Ng W, Lu A (2007) Fg-index: towards verification-free query processing on graph databases. In: Proceedings of the ACM SIGMOD international conference on Management of data. SIGMOD'07, 857-872.
19. Yan X, Yu P, Han J (2004) Graph indexing: a frequent structure-based approach. In: Proceedings of the ACM SIGMOD international conference on Management of data. SIGMOD'04, 335-346.
20. Williams DW, Huan J, Wang W (2007) Graph database indexing using structured graph decomposition. Data Engineering, 2007 ICDE 2007 IEEE 23rd International Conference on: 976-985.
21. Ferro A, Giugno R, Mongiovì M, Pulvirenti A, Skripin D, et al. (2008) Graphfind: enhancing graph searching by low support data mining techniques. BMC bioinformatics 9: S10.
22. Cohen E, Datar M, Fujiwara S, Gionis A, Indyk P, et al. (2001) Finding interesting associations without support pruning. IEEE Transactions on Knowledge and Data Engineering 13: 64-78.
23. Zhao P, Yu JX, Yu PS (2007) Graph indexing: tree+delta ≤ graph. VLDB'07: Proceedings of the 33rd international conference on Very large data bases: 938-949.
24. Kriege N, Mutzel P (2011) Ct-index: Fingerprint-based graph indexing combining cycles and trees. In: Proceeding of the IEEE International Conference on Data Engineering. ICDE'11, 1115-1126.
25. Dean J, Ghemawat S, (2004) MapReduce: Simplified data processing on large clusters. In: Proc. Of Operating Systems Design and Implementation (OSDI' 04): 137-150.
26. National cancer institute, available: http://www.nci.nih.gov/, accessed 2013 marc 10.
27. He Y, Lin F, Chipman P, Bator C, Baker T, et al. (2002) Structure of decay-accelerating factor bound to echovirus 7: a virus-receptor complex. Proc Natl Acad Sci USA 99: 10325-10329.
28. Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, et al. (2011) Cmview: Interactive contact map visualization and analysis. Bioinformatics 27: 1573-1577.
29. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. Nature genetics 25: 25-29.
30. Zhang C, Hanspers Z, Kuchinsky A, Salomonis N, Xu D, et al. (2013) Mosaic: Making biological sense of complex networks. BIOINFORMATICS 28: 1943-4.