Skip Navigation



Bioinformatics Advance Access published online on September 3, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti015
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/3/293    most recent
bti015v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Haft, D. H.
Right arrow Articles by White, O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Haft, D. H.
Right arrow Articles by White, O.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received May 5, 2004
Revised July 9, 2004
Accepted August 5, 2004

Article

Genome properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics

Daniel H. Haft 1, Jeremy D. Selengut 1*, Lauren M. Brinkac 1, Nikhat Zafar 1, and Owen White 1

1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850

* To whom correspondence should be addressed.


  Abstract

Motivation: The presence or absence of metabolic pathways, and structures provides context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics.

Results: We have created Genome Properties to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny, and computational analyses. The results of searches using Hidden Markov Models (HMMs) allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports, and other forms of evidence. Genome Properties has been applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties.

Availability: Genome Properties can be found at http://www.tigr.org/Genome_Properties.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
T. Davidsen, E. Beck, A. Ganapathy, R. Montgomery, N. Zafar, Q. Yang, R. Madupu, P. Goetz, K. Galinsky, O. White, et al.
The comprehensive microbial resource
Nucleic Acids Res., November 5, 2009; (2009) gkp912v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. M. Brinkac, T. Davidsen, E. Beck, A. Ganapathy, E. Caler, R. J. Dodson, A. S. Durkin, D. M. Harkins, H. Lorenzi, R. Madupu, et al.
Pathema: a clade-specific bioinformatics resource center for pathogen research
Nucleic Acids Res., October 20, 2009; (2009) gkp850v1.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
J. M. Greene, F. Collins, E. J. Lefkowitz, D. Roos, R. H. Scheuermann, B. Sobral, R. Stevens, O. White, and V. Di Francesco
National Institute of Allergy and Infectious Diseases Bioinformatics Resource Centers: New Assets for Pathogen Informatics
Infect. Immun., July 1, 2007; 75(7): 3212 - 3219.
[Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. D. Selengut, D. H. Haft, T. Davidsen, A. Ganapathy, M. Gwinn-Giglio, W. C. Nelson, A. R. Richter, and O. White
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D260 - D264.
[Abstract] [Full Text] [PDF]

Home page
 Proc Am Thorac SocHome page
Y. A. Lussier and Y. Liu
Computational Approaches to Phenotyping: High-Throughput Phenomics
Proceedings of the ATS, January 1, 2007; 4(1): 18 - 25.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
R. Seshadri, S. W. Joseph, A. K. Chopra, J. Sha, J. Shaw, J. Graf, D. Haft, M. Wu, Q. Ren, M. J. Rosovitz, et al.
Genome Sequence of Aeromonas hydrophila ATCC 7966T: Jack of All Trades
J. Bacteriol., December 1, 2006; 188(23): 8272 - 8282.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. H. Badger, T. R. Hoover, Y. V. Brun, R. M. Weiner, M. T. Laub, G. Alexandre, J. Mrazek, Q. Ren, I. T. Paulsen, K. E. Nelson, et al.
Comparative Genomic Evidence for a Close Relationship between the Dimorphic Prosthecate Bacteria Hyphomonas neptunium and Caulobacter crescentus.
J. Bacteriol., October 1, 2006; 188(19): 6841 - 6850.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. Y. Gerdes, O. V. Kurnasov, K. Shatalin, B. Polanuyer, R. Sloutsky, V. Vonstein, R. Overbeek, and A. L. Osterman
Comparative Genomics of NAD Biosynthesis in Cyanobacteria.
J. Bacteriol., April 1, 2006; 188(8): 3012 - 3023.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Liolios, N. Tavernarakis, P. Hugenholtz, and N. C. Kyrpides
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D332 - D334.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Overbeek, T. Begley, R. M. Butler, J. V. Choudhuri, H.-Y. Chuang, M. Cohoon, V. de Crecy-Lagard, N. Diaz, T. Disz, R. Edwards, et al.
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Nucleic Acids Res., October 7, 2005; 33(17): 5691 - 5702.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
V. Joardar, M. Lindeberg, R. W. Jackson, J. Selengut, R. Dodson, L. M. Brinkac, S. C. Daugherty, R. DeBoy, A. S. Durkin, M. G. Giglio, et al.
Whole-Genome Sequence Analysis of Pseudomonas syringae pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition
J. Bacteriol., September 15, 2005; 187(18): 6488 - 6498.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
D. Field, E. J. Feil, and G. A. Wilson
Databases and software for the comparison of prokaryotic genomes
Microbiology, July 1, 2005; 151(7): 2125 - 2132.
[Abstract] [Full Text] [PDF]

Home page
 Reviews in Mineralogy and GeochemistryHome page
K. E. Nelson and B. Methe
Metabolism and Genomics: Adventures Derived From Complete Genome Sequencing
Reviews in Mineralogy and Geochemistry, January 1, 2005; 59(1): 279 - 294.
[Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.