Data mining pathogen genomes using GeneOrder and CoreGenes: Gene order, synteny, and proteomes

Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008

Volumn , Issue , 2008, Pages 234-240

  Mahadevan, Padmanabhan ^a   Seto, Donald ^a  

^a GEORGE MASON UNIVERSITY   (United States)

Author keywords

Comparative genomics; E. coli; GeneOrder; Hypothetical protein annotation; Pathogen

Indexed keywords

BACTERIAL GENOMES; BACTERIAL PATHOGENS; COMPARATIVE GENOMICS; E. COLI; EXPONENTIAL RATES; GENE ORDERS; GENEORDER; GENOME ANNOTATIONS; GENOME SEQUENCES; HUMAN HEALTHS; HYPOTHETICAL PROTEIN ANNOTATION; MULTIPLE SEQUENCES; ON THE FLIES; PROTEOMES; SEQUENCE DATUM; SYNTENY; USER-FRIENDLY TOOLS;

BACTERIOLOGY; BIOINFORMATICS; ESCHERICHIA COLI; INFORMATION MANAGEMENT; NUCLEIC ACIDS;

PATHOGENS;

EID: 62649140227     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (22)

1. Tamames J. (2001). Evolution of gene order conservation in prokaryotes. Genome Biology 2, 1-11.
2. Overbeek R, Fonstein M, D'Souza M, Pusch GD and Maltsev N. (1999). The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96, 2896-2901.
3. Zheng Y, Roberts RJ and Kasif S. (2002). Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biology 3, 1-9.
4. Tamames J, Gonzalez-Moreno M, Mingorance J, Valencia A and Vicente M. (2001). Bringing gene order into bacterial shape. Trends in Genetics 17, 124-6.
5. Bentley SD and Parkhill J. (2004). Comparative genomic structure of prokaryotes. Annu. Rev. Genet. 38, 771-91.
6. Liolios K, Mavromatis K, Tavernarakis N and Kyrpides NC. (2008). The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. D475-9.
7. Kaluszka A and Gibas C. (2004). Interactive geneorder comparison of multiple genomes. Bioinformatics 20, 3662-4.
8. Sakharkar KR and Chow VT. (2004). Exploring genome architecture through GOV: a WWW-based gene order visualizer. Bioinformatics 20, 984-5.
9. Pavesi G, Mauri G, Iannelli F, Gissi C and Pesole G. (2004). GeneSyn: a tool for detecting conserved gene order across genomes. Bioinformatics 20, 1472-4.
10. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG and Parkhill J. (2005). ACT: the Artemis Comparison Tool. Bioinformatics 21, 3422-3.
11. Haas BJ, Delcher AL, Wortman JR and Salzberg SL. (2004). DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20, 3643-6.
12. Sinha AU and Meller J. (2007). Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics 8, 82.
13. Kozik A, Kochetkova E and Michelmore R. (2002). GenomePixelizer-a visualization program for comparative genomics within and between species. Bioinformatics 18, 335-6.
14. Kent WJ. (2002). BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-64.
15. Celamkoti S, Kundeti S, Purkayastha A, Mazumder R, Buck C and Seto D. (2004). GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes. BMC Bioinformatics 5, 52.
16. Gish W. (1996-2004). http://blast.wustl.edu
17. Zafar N, Mazumder R and Seto D. (2002). CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinformatics 3, 12.
18. Cai CZ, Han LY, Ji ZL, Chen X and Chen YZ. (2003). SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res. 31, 3692-3697.
19. Kaper JB, Nataro JP and Mobley HLT. (2004). Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123-40.
20. Deng W, Liou S-R, Plunkett III G, Mayhew GF, Rose DJ, Burland V, Kodoyianni V, Schwartz DC and Blattner FR. (2003). Comparative Genomics of Salmonella enterica Serovar Typhi Strains Ty2 and CT18. J. Bacteriol. 185, 2330-7.
21. Schaecher SR, Mackenzie JM and Pekosz A. (2007). The ORF7b protein of severe acute respiratory syndrome coronavirus (SARS) is expressed in virus-infected cells and incorporated into SARS-CoV particles. J. Virol. 81, 718-31.
22. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG and Thompson JD. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497-500.