CoreGenes3.5: A webserver for the determination of core genes from sets of viral and small bacterial genomes

BMC Research Notes

Volumn 6, Issue 1, 2013, Pages

  Turner, Dann ^a   Reynolds, Darren ^a   Seto, Donald ^b   Mahadevan, Padmanabhan ^c  

^a UNIVERSITY OF THE WEST OF ENGLAND   (United Kingdom)

^b GEORGE MASON UNIVERSITY   (United States)

^c UNIVERSITY OF TAMPA   (United States)

Author keywords

Bacteriophage; Core genes; Data mining; Taxonomy; Viral genomics

Indexed keywords

BACTERIA (MICROORGANISMS);

ALGORITHM; ARTICLE; BACTERIAL GENOME; BIOLOGY; COMPUTER PROGRAM; DATA MINING; GENETIC DATABASE; GENOMICS; INTERNET; METHODOLOGY; PHYLOGENY; VIRUS GENOME; PROCEDURES;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; GENOME, BACTERIAL; GENOME, VIRAL; GENOMICS; INTERNET; PHYLOGENY; SOFTWARE;

EID: 84875845952     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-6-140     Document Type: Article

References (21)

1. Pan-Genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. Liang W, Zhao Y, Chen C, Cui X, Yu J, Xiao J, Kan B, PLoS One 2012 7 45346
2. The ac53, ac78, ac101 and ac103 are newly discovered core genes in the family Baculoviridae. Garavaglia MJ, Miele SAB, Iserte JA, Belaich MN, Ghiringhelli PD, J Virol 2012 86 12069 12079
3. Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes. Yutin N, Koonin EV, Virol J 2012 9 161
4. Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes. Mahadevan P, King JF, Seto D, Int J Comput Biol Drug Des 2009 2 100 114
5. The cyanobacterial genome core and the origin of photosynthesis. Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY, Proc Natl Acad Sci USA 2006 103 13126 13131 (Pubitemid 44338927)
6. Classification of Myoviridae bacteriophages using protein sequence similarity. Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM, BMC Microbiol 2009 9 224
7. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Lavigne R, Seto D, Mahadevan P, Ackermann H-W, Kropinski AM, Res Microbiol 2008 159 406 414
8. Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes. Mahadevan P, Seto D, Adv Exp Med Biol 2010 680 379 385
9. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. Zafar N, Mazumder R, Seto D, BMC Bioinforma 2002 3 12
10. CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb. Mahadevan P, King JF, Seto D, BMC Res Notes 2009 2 168
11. mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. Shao Y, He X, Harrison EM, Tai C, Ou H-Y, Rajakumar K, Deng Z, Nucleic Acids Res 2010 38 194 200
12. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Parra G, Bradnam K, Korf I, Bioinformatics 2007 23 1061 1067 (Pubitemid 47050556)
13. nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms. Yao J, Lin H, Doddapaneni H, Civerolo EL, In Silico Biol (Gedrukt) 2007 7 195 200 (Pubitemid 47335235)
14. GenomeBlast: a web tool for small genome comparison. Lu G, Jiang L, Helikar RMK, Rowley TW, Zhang L, Chen X, Moriyama EN, BMC Bioinforma 2006 7 Suppl 4 18
15. Interactive gene-order comparison for multiple small genomes. Kaluszka A, Gibas C, Bioinformatics 2004 20 3662 3664 (Pubitemid 40136809)
16. Bacteriophages with the ability to degrade uropathogenic Escherichia coli biofilms. Chibeu A, Lingohr EJ, Masson L, Manges A, Harel J, Ackermann H-W, Kropinski AM, Boerlin P, Viruses 2012 4 471 487
17. Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3. Kropinski AM, Van den Bossche A, Lavigne R, Noben J-P, Babinger P, Schmitt R, Virol J 2012 9 102
18. Complete genome of the broad-host-range Erwinia amylovora phage phiEa21-4 and its relationship to Salmonella phage felix O1. Lehman SM, Kropinski AM, Castle AJ, Svircev AM, Appl Environ Microbiol 2009 75 2139 2147
19. The genome and proteome of a virulent Escherichia coli O157:H7 bacteriophage closely resembling Salmonella phage Felix O1. Villegas A, She Y-M, Kropinski AM, Lingohr EJ, Mazzocco A, Ojha S, Waddell TE, Ackermann H-W, Moyles DM, Ahmed R, Johnson RP, Virol J 2009 6 41
20. GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes. Celamkoti S, Kundeti S, Purkayastha A, Mazumder R, Buck C, Seto D, BMC Bioinforma 2004 5 52
21. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. Mahadevan P, Seto D, BMC Res Notes 2010 3 41