Genome-wide operon prediction in Staphylococcus aureus

Nucleic Acids Research
Liangsu WangCarlos Zamudio

Abstract

Identification of operon structure is critical to understanding gene regulation and function, and pathogenesis, and for identifying targets towards the development of new antibiotics in bacteria. Recently, the complete genome sequences of a large number of important human bacterial pathogens have become available for computational analysis, including the major human Gram-positive pathogen Staphylococcus aureus. By annotating the predicted operon structure of the S.aureus genome, we hope to facilitate the exploration of the unique biology of this organism as well as the comparative genomics across a broad range of bacteria. We have integrated several operon prediction methods and developed a consensus approach to score the likelihood of each adjacent gene pair to be co-transcribed. Gene pairs were separated into distinct operons when scores were equal to or below an empirical threshold. Using this approach, we have generated a S.aureus genome map with scores annotated at the intersections of every adjacent gene pair. This approach predicted about 864 monocistronic transcripts and 533 polycistronic operons from the protein-encoding genes in the S.aureus strain Mu50 genome. When compared with a set of experimentally determined S.a...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 25, 1985·Nucleic Acids Research·G Zurawski, S M Zurawski
Feb 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·S LöfdahlM Lindberg
May 25, 1984·Nucleic Acids Research·V Brendel, E N Trifonov
Jan 1, 1980·Molecular & General Genetics : MGG·T Sako, Y Sakakibara
Apr 1, 1996·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·U KoppH Labischinski
Jul 1, 1996·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·A M StrandénB Berger-Bächi
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Sep 5, 1997·Science·F R BlattnerY Shao
Feb 21, 1998·Nucleic Acids Research·A M HuertaJ Collado-Vides
Apr 1, 1998·Bioinformatics·T L Bailey, M Gribskov
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·R OverbeekN Maltsev
May 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·H SalgadoJ Collado-Vides
Aug 5, 2000·Journal of Molecular Biology·M D ErmolaevaS L Salzberg
Nov 28, 2000·Journal of Bacteriology·S GertzM Hecker
Feb 7, 2001·Applied and Environmental Microbiology·G CabreraR K Jayaswal
Feb 17, 2001·Infection and Immunity·S B ReedK W Bayles
Feb 27, 2001·Nucleic Acids Research·M D ErmolaevaS L Salzberg
Mar 21, 2001·Antimicrobial Agents and Chemotherapy·R S WashburnD R Gentry
Nov 3, 2001·Genome Research·R Friedman, A L Hughes
Jan 26, 2002·Nucleic Acids Research·Shyam UnniramanValakunja Nagaraja
Apr 16, 2002·Molecular Microbiology·R Allyn ForsythJudith W Zyskind

❮ Previous
Next ❯

Citations

Jul 4, 2012·Briefings in Functional Genomics·Li-Yeh ChuangCheng-Hong Yang
Apr 19, 2008·Briefings in Bioinformatics·Rutger W W BrouwerSacha A F T van Hijum
Oct 26, 2007·Nucleic Acids Research·Salim CharaniyaWei-Shou Hu
Feb 13, 2010·Nucleic Acids Research·Nicole J P ten Broeke-SmitsC H Edwin Boel
Apr 14, 2010·Nucleic Acids Research·Li-Yeh ChuangCheng-Hong Yang
Aug 2, 2006·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Ling XuDavid W Rice
Jan 27, 2006·Antimicrobial Agents and Chemotherapy·Katherine YoungJun Wang
Nov 24, 2006·Applied and Environmental Microbiology·Nicholas H BergmanZhaohui S Qin
Dec 13, 2006·Infection and Immunity·Patrick H Tu QuocWilliam L Kelley
Feb 19, 2008·Journal of Bacteriology·Timothy C MeredithSuzanne Walker
Jun 24, 2008·Journal of Bacteriology·Nouri L Ben ZakourYves Le Loir
May 5, 2006·Journal of Bacteriology·Tomaz KoprivnjakJerrold P Weiss
Sep 26, 2008·BMC Bioinformatics·Anis Karimpour-FardLawrence E Hunter
Jun 30, 2007·BMC Genomics·Hirokazu KobayashiShigehiko Kanaya
Jan 26, 2012·BMC Microbiology·Bettina SchulthessBrigitte Berger-Bächi
Jun 22, 2006·Journal of Molecular Evolution·Alberto J L MacarioEverly Conway de Macario
Nov 5, 2014·Proceedings of the National Academy of Sciences of the United States of America·Yue DingLefu Lan
Sep 18, 2007·Artificial Intelligence in Medicine·Shuqin WangYanchun Liang
Jul 25, 2006·Molecular Microbiology·Anthony R RichardsonFerric C Fang
May 24, 2012·Phytotherapy Research : PTR·Jesus A CuaronJohn E Gustafson
Jan 5, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Li-Yeh ChuangCheng-Hong Yang
May 24, 2006·Computational Biology and Chemistry·Guo-qing ZhangYi-xue Li
Apr 29, 2006·International Journal of Medical Microbiology : IJMM·Jan Pané-FarréMichael Hecker
Sep 24, 2016·Briefings in Functional Genomics·Syed Shujaat Ali Zaidi, Xuegong Zhang
Apr 26, 2019·PLoS Computational Biology·Hatice AkarsuLaurent Falquet

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

© 2022 Meta ULC. All rights reserved