Home   |  About Startbioinfo | Other web-portals 

Categories of resources

Suggested Readings
 
 
Total resources - 14
A comparative account of pathways, feature-validations and application-based categorizations : Pathways in virus
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
CPA - Comparative Pathway Analyzer
http://cpa.cebitec.uni-bielefeld.de
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.
2008
100
EMP - Enzymes and Metabolic Pathways Database
http://www.empproject.com
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.
1996
100
URL could not be retrieved (10/01/2012).
ERGO - ERGO Genome Analysis and Discovery System
http://www.ergo-light.com
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.
2003
100
GON - Genomic Object Net
http://genome.ib.sci.yamaguchi-u.ac.jp/~gon/index
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.
2000
100
IMG - Integrated Microbial Genomes
http://img.jgi.doe.gov
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.
2007
100
METAPATH
http://scopes.biologie.hu-berlin.de/index.php?m=path
Calculation of minimal synthesis pathway.
Handorf T, Ebenhöh 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.
2007
100
MiMI - Michigan Molecular Interactions
http://mimi.ncibi.org/MimiWeb/main-page.jsp
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.
2006
100
NCBI BioSystems
http://www.ncbi.nlm.nih.gov/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.
2009
100
P2CS - Prokaryotic 2-Component Systems
http://www.p2cs.org
Database of prokaryotic two-component system signal transduction proteins.
Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, Méjean 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.
2009
100
Pathway Commons
http://www.pathwaycommons.org/pc/
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.
2010
100
Protein Lounge
http://www.proteinlounge.com
Contains curated pathways for many different organisms.
Not available
Not available
100
The SEED
http://theseed.uchicago.edu/FIG/index.cgi
Annotation and analysis tool for microbial genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-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, Rückert 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.
2005
100
VirHostNet
http://pbildb1.univ-lyon1.fr/virhostnet/login.php
Knowledgebase system for curation, analysis and management of virus-host molecular interactions.
Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, André 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.
2009
100
VisANT
http://visant.bu.edu
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.
2004
100
 
Disclaimer
Grow and let grow!
copyright © shodhaka life sciences private limited; all rights reserved

Internet Coupons
xanga traffic