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Total resources - 14
A comparative account of pathways, feature-validations and application-based categorizations : Pathways in virus
S.NoResources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
1 CPA - Comparative Pathway Analyzer
Investigates reaction content of a set of organisms.
Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A. Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W433-7. Epub 2008 Jun 6. PubMed PMID: 18539612; PubMed Central PMCID: PMC2447754.
2 EMP - Enzymes and Metabolic Pathways Database
Electronic source of biochemical data that stores details like chemical reactions and Km.
Selkov E, Basmanova S, Gaasterland T, Goryanin I, Gretchkin Y, Maltsev N, Nenashev V, Overbeek R, Panyushkina E, Pronevitch L, Selkov E Jr, Yunus I. The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Res. 1996 Jan 1;24(1):26-8. PubMed PMID: 8594593; PubMed Central PMCID: PMC145618.
URL could not be retrieved (10/01/2012).
URL could not be retrieved (10/01/2012).
3 ERGO - ERGO Genome Analysis and Discovery System
Curated database of genomic DNA with functional annotation and pathway information.
Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P,KapatralV,Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. The ERGO genome analysis and discovery system. Nucleic Acids Res. 2003 Jan 1;31(1):164-71. PubMed PMID: 12519973; PubMed Central PMCID: PMC165577.
4 GON - Genomic Object Net
Software platform for biological pathway modeling and simulation.
Matsuno H, Doi A, Nagasaki M, Miyano S. Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput. 2000:341-52. PubMed PMID: 10902182.
5 IMG - Integrated Microbial Genomes
Data management, analysis and annotation platform for all publicly available genomes.
Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. Epub 2007 Oct 12. PubMed PMID: 17933782; PubMed Central PMCID: PMC2238897.
Calculation of minimal synthesis pathway.
Handorf T, EbenhF6h O. MetaPath Online: a web server implementation of the network expansion algorithm. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W613-8. Epub 2007 May 5. PubMed PMID: 17483511; PubMed Central PMCID:PMC1933239.
7 MiMI - Michigan Molecular Interactions
Contains pathway diagrams from KEGG and Reactome.
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720.
8 NCBI BioSystems
Connects biosystem records with the associated literature, molecular and chemical data.
Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ. MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol. 2009;10(8):R84. Epub 2009 Aug 14. PubMed PMID: 19682380; PubMed Central PMCID:PMC2745765.
9 P2CS - Prokaryotic 2-Component Systems
Database of prokaryotic two-component system signal transduction proteins.
Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, M\E9jean V, Whitworth DE. P2CS: a two-component system resource for prokaryotic signal transduction research. BMC Genomics. 2009 Jul 15;10:315. PubMed PMID: 19604365 ; PubMed Central PMCID: PMC2716373.
10 Pathway Commons
Provides researchers with convenient access to the collection of publicly available pathways from many different organisms.
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. Epub 2010 Nov 10. PubMed PMID: 21071392; PubMed Central PMCID: PMC3013659.
11 Protein Lounge
Contains curated pathways for many different organisms.
Not available
Not available
12 The SEED
Annotation and analysis tool for microbial genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Cr\E9cy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A,Portnoy V, Pusch GD, Rodionov DA, RFCckert C, Steiner J, Stevens R, Thiele I,Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005. PubMed PMID: 16214803; PubMed Central PMCID: PMC1251668.
13 VirHostNet
Knowledgebase system for curation, analysis and management of virus-host molecular interactions.
Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, Andr\E9 P, LotteauV, Rabourdin-Combe C. VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res.2009 Jan ; 37(Database issue):D661-8. Epub 2008 Nov 4. PubMed PMID: 18984613;PubMed Central PMCID: PMC2686459.
14 VisANT
Visual analysis tool for biological networks, predict the function of a network module.
Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004 Feb 19;5:17. PubMed PMID: 15028117; PubMed Central PMCID: PMC368431.
copyright © Dr. Kshitish Acharya K; all rights reserved

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