CAMBer: An approach to support comparative analysis of multiple bacterial strains

BMC Genomics

Volumn 12, Issue SUPPL.2, 2011, Pages

  Wozniak, Michal ^a,b   Wong, Limsoon ^b   Tiuryn, Jerzy ^a  

^a UNIVERSITY OF WARSAW   (Poland)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL STRAIN; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER PROGRAM; CONTROLLED STUDY; ESCHERICHIA COLI; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; MATHEMATICAL ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; STAPHYLOCOCCUS AUREUS; TRANSLATION INITIATION; UNINDEXED SEQUENCE; BIOLOGY; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER GRAPHICS; GENETICS; MOLECULAR GENETICS; MULTIGENE FAMILY; START CODON; TIME;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MYCOBACTERIUM TUBERCULOSIS; STAPHYLOCOCCUS;

CODON, INITIATOR; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; ESCHERICHIA COLI; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; MYCOBACTERIUM TUBERCULOSIS; SOFTWARE; STAPHYLOCOCCUS AUREUS; TIME FACTORS;

EID: 79960886963     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S2-S6     Document Type: Article

References (24)

1. Zheng H, Lu L, Wang B, Pu S, Zhang X, Zhu G, Shi W, Zhang L, Wang H, Wang S, Zhao G, Zhang Y. Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv. PLoS One 2008, 3(6):e2375. 10.1371/journal.pone.0002375, 2440308, 18584054.
2. Feng J, Lupien A, Gingras H, Wasserscheid J, Dewar K, Légaré D, Ouellette M. Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance. Genome Research 2009, 19(7):1214-1223. 10.1101/gr.089342.108, 2704432, 19351617.
3. Andries K, Verhasselt P, Guillemont J, Göhlmann HWH, Neefs JM, Winkler H, Van Gestel J, Timmerman P, Zhu M, Lee E, Williams P, de Chaffoy D, Huitric E, Hoffner S, Cambau E, Truffot-Pernot C, Lounis N, Jarlier V. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 2005, 307(5707):223-227. 10.1126/science.1106753, 15591164.
4. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol 2010, 60(4):708-720. 10.1007/s00248-010-9717-3, 2974192, 20623278.
5. Wakaguri H, Suzuki Y, Sasaki M, Sugano S, Watanabe J. Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs. BMC Genomics 2009, 10:312. 10.1186/1471-2164-10-312, 2722674, 19602295.
6. Boneca IG, de Reuse H, Epinat JC, Pupin M, Labigne A, Moszer I. A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Research 2003, 31(6):1704-1714. 10.1093/nar/gkg250, 152854, 12626712.
7. Park J, Teichmann SA, Hubbard T, Chothia C. Intermediate sequences increase the detection of homology between sequences. Journal of Molecular Biology 1997, 273:349-354. 10.1006/jmbi.1997.1288, 9367767.
8. Schlueter SD, Wilkerson MD, Huala E, Rhee SY, Brendel V. Community-based gene structure annotation. Trends Plant Sci 2005, 10:9-14. 10.1016/j.tplants.2004.11.002, 15642518.
9. van den Boogaard J, Kibiki GS, Kisanga ER, Boeree MJ, Aarnoutse RE. New drugs against tuberculosis: Problems, progress, and evaluation of agents in clinical development. Antimicrob Agents Chemother 2009, 53(3):849-862. 10.1128/AAC.00749-08, 2650526, 19075046.
10. Overbeek R, Begley T, B RM, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic acids research 2005, 33(17):5691-5702. 10.1093/nar/gki866, 1251668, 16214803.
11. Disz T, Akhter S, D C, et al. Accessing the SEED genome databases via Web services API: Tools for programmers. BMC Bioinformatics 2010, 11:319+. 10.1186/1471-2105-11-319, 2900279, 20546611.
12. Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV. Genome alignment, evolution of prokaryotic genome organization and prediction of gene function using genomic context. Genome Research 2001, 11:356-372. 10.1101/gr.GR-1619R, 11230160.
13. Wozniak M, Wong L, Tiuryn J. CAMBer: an approach to support comparative analysis of multiple bacterial strains. Proceedings of the International Conference on Bioinformatics and Biomedicine: 18-21 December 2010; Hong Kong 2010, 121-126.
14. Rost B. Twilight zone of protein sequence alignments. Protein engineering 1999, 12(2):85-94. 10.1093/protein/12.2.85, 10195279.
15. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2011, 39(Database issue):D32-D37. 3013681, 21071399.
16. Ioerger TR, Koo S, No EG, Chen X, Larsen MH, Jacobs WR, Pillay M, Sturm AW, Sacchettini JC. Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa. PLoS ONE 2009, 4(11):e7778. 10.1371/journal.pone.0007778, 2767505, 19890396.
17. Fleischmann RD, Alland D, Eisen JA, et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. Journal of Bacteriology 2002, 184(19):5479-5490. 10.1128/JB.184.19.5479-5490.2002, 135346, 12218036.
18. Cole S, Brosch R, Parkhill J, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393(6685):537-544. 10.1038/31159, 9634230.
19. Chambers HF. The changing epidemiology of Staphylococcus aureus?. Emerging infectious diseases 2001, 7(2):178-182. 10.3201/eid0702.010204, 2631711, 11294701.
20. Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, Lian J, Ito T, Kanamori M, Matsumaru H, Maruyama A, Murakami H, Hosoyama A, Mizutani-Ui Y, Takahashi NK, Sawano T, Inoue R, Kaito C, Sekimizu K, Hirakawa H, Kuhara S, Goto S, Yabuzaki J, Kanehisa M, Yamashita A, Oshima K, Furuya K, Yoshino C, Shiba T, Hattori M, Ogasawara N, Hayashi H, Hiramatsu K. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 2001, 357(9264):1225-1240. 10.1016/S0140-6736(00)04403-2, 11418146.
21. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. The complete genome sequence of Escherichia coli K-12. Science 1997, 277(5331):1453-1462. 10.1126/science.277.5331.1453, 9278503.
22. Sacerdot C, et al. Sequence of a 1.26-kb DNA fragment containing the structural gene for E. coli initiation factor IF3: presence of an AUU initiator codon. EMBO 1982, 1(3):311-315. 553041, 6325158.
23. Missiakas D, Georgopoulos C, Raina S. The Escherichia coli heat shock gene htpY: mutational analysis, cloning, sequencing, and transcriptional regulation. Journal of Bacteriology 1993, 175(9):2613-2624. 204563, 8478327.
24. Sabath N, Price N, Graur D. A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives. Virology Journal 2009, 6:144+. 10.1186/1743-422X-6-144, 2754452, 19761605.