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Literature DB >> 11125067

The Comprehensive Microbial Resource.

J D Peterson¹, L A Umayam, T Dickinson, E K Hickey, O White.

Abstract

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.

Mesh：

Year: 2001 PMID： 11125067 PMCID： PMC29848 DOI： 10.1093/nar/29.1.123

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

9 in total

1. TIGRFAMs: a protein family resource for the functional identification of proteins.

Authors: D H Haft; B J Loftus; D L Richardson; F Yang; J A Eisen; I T Paulsen; O White
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

2. Improved microbial gene identification with GLIMMER.

Authors: A L Delcher; D Harmon; S Kasif; O White; S L Salzberg
Journal: Nucleic Acids Res Date: 1999-12-01 Impact factor: 16.971

3. The COG database: a tool for genome-scale analysis of protein functions and evolution.

Authors: R L Tatusov; M Y Galperin; D A Natale; E V Koonin
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

4. Skewed oligomers and origins of replication.

Authors: S L Salzberg; A J Salzberg; A R Kerlavage; J F Tomb
Journal: Gene Date: 1998-09-14 Impact factor: 3.688

Review 5. Profile hidden Markov models.

Authors: S R Eddy
Journal: Bioinformatics Date: 1998 Impact factor: 6.937

6. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.

Authors: H P Klenk; R A Clayton; J F Tomb; O White; K E Nelson; K A Ketchum; R J Dodson; M Gwinn; E K Hickey; J D Peterson; D L Richardson; A R Kerlavage; D E Graham; N C Kyrpides; R D Fleischmann; J Quackenbush; N H Lee; G G Sutton; S Gill; E F Kirkness; B A Dougherty; K McKenney; M D Adams; B Loftus; S Peterson; C I Reich; L K McNeil; J H Badger; A Glodek; L Zhou; R Overbeek; J D Gocayne; J F Weidman; L McDonald; T Utterback; M D Cotton; T Spriggs; P Artiach; B P Kaine; S M Sykes; P W Sadow; K P D'Andrea; C Bowman; C Fujii; S A Garland; T M Mason; G J Olsen; C M Fraser; H O Smith; C R Woese; J C Venter
Journal: Nature Date: 1997-11-27 Impact factor: 49.962

7. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

Authors: O White; J A Eisen; J F Heidelberg; E K Hickey; J D Peterson; R J Dodson; D H Haft; M L Gwinn; W C Nelson; D L Richardson; K S Moffat; H Qin; L Jiang; W Pamphile; M Crosby; M Shen; J J Vamathevan; P Lam; L McDonald; T Utterback; C Zalewski; K S Makarova; L Aravind; M J Daly; K W Minton; R D Fleischmann; K A Ketchum; K E Nelson; S Salzberg; H O Smith; J C Venter; C M Fraser
Journal: Science Date: 1999-11-19 Impact factor: 47.728

8. Prediction of transcription terminators in bacterial genomes.

Authors: M D Ermolaeva; H G Khalak; O White; H O Smith; S L Salzberg
Journal: J Mol Biol Date: 2000-08-04 Impact factor: 5.469

9. Alignment of whole genomes.

Authors: A L Delcher; S Kasif; R D Fleischmann; J Peterson; O White; S L Salzberg
Journal: Nucleic Acids Res Date: 1999-06-01 Impact factor: 16.971

9 in total

189 in total

1. TIGRFAMs: a protein family resource for the functional identification of proteins.

Authors: D H Haft; B J Loftus; D L Richardson; F Yang; J A Eisen; I T Paulsen; O White
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

2. AraC-XylS database: a family of positive transcriptional regulators in bacteria.

Authors: Raquel Tobes; Juan L Ramos
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

3. The genome of M. acetivorans reveals extensive metabolic and physiological diversity.

Authors: James E Galagan; Chad Nusbaum; Alice Roy; Matthew G Endrizzi; Pendexter Macdonald; Will FitzHugh; Sarah Calvo; Reinhard Engels; Serge Smirnov; Deven Atnoor; Adam Brown; Nicole Allen; Jerome Naylor; Nicole Stange-Thomann; Kurt DeArellano; Robin Johnson; Lauren Linton; Paul McEwan; Kevin McKernan; Jessica Talamas; Andrea Tirrell; Wenjuan Ye; Andrew Zimmer; Robert D Barber; Isaac Cann; David E Graham; David A Grahame; Adam M Guss; Reiner Hedderich; Cheryl Ingram-Smith; H Craig Kuettner; Joseph A Krzycki; John A Leigh; Weixi Li; Jinfeng Liu; Biswarup Mukhopadhyay; John N Reeve; Kerry Smith; Timothy A Springer; Lowell A Umayam; Owen White; Robert H White; Everly Conway de Macario; James G Ferry; Ken F Jarrell; Hua Jing; Alberto J L Macario; Ian Paulsen; Matthew Pritchett; Kevin R Sowers; Ronald V Swanson; Steven H Zinder; Eric Lander; William W Metcalf; Bruce Birren
Journal: Genome Res Date: 2002-04 Impact factor: 9.043

Review 4. Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry.

Authors: Peter J Kennelly
Journal: Biochem J Date: 2003-03-01 Impact factor: 3.857

5. MBGD: microbial genome database for comparative analysis.

Authors: Ikuo Uchiyama
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli.

Authors: Kevin J Cheung; Vasudeo Badarinarayana; Douglas W Selinger; Daniel Janse; George M Church
Journal: Genome Res Date: 2003-02 Impact factor: 9.043

The Comprehensive Microbial Resource.

1. TIGRFAMs: a protein family resource for the functional identification of proteins.

2. Improved microbial gene identification with GLIMMER.

3. The COG database: a tool for genome-scale analysis of protein functions and evolution.

4. Skewed oligomers and origins of replication.

Review 5. Profile hidden Markov models.

6. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.

7. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

8. Prediction of transcription terminators in bacterial genomes.

9. Alignment of whole genomes.

1. TIGRFAMs: a protein family resource for the functional identification of proteins.

2. AraC-XylS database: a family of positive transcriptional regulators in bacteria.

3. The genome of M. acetivorans reveals extensive metabolic and physiological diversity.

Review 4. Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry.

5. MBGD: microbial genome database for comparative analysis.

6. A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli.

7. PROBEmer: A web-based software tool for selecting optimal DNA oligos.

8. Comparative immunopeptidomics of humans and their pathogens.

9. Trends between gene content and genome size in prokaryotic species with larger genomes.

10. Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.