SpringerProtocols: Abstract: 6. In Sffamily Identification of Genes in Bacteriophage DNA

6. In Sffamily Identification of Genes in Bacteriophage DNA

By: Andrew M. Kropinski^{4 5 6}, Mark Borodovsky⁷, Tim J. Carver⁸, Ana M. Cerdeño-Tárraga⁹, Aaron Darling¹⁰, Alexandre Lomsadze¹¹, Padmanabhan Mahadevan¹², Paul Stothard¹³, Donald Seto¹⁴, Gary Van Domselaar¹⁵, David S. Wishart¹⁶

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One of the most satisfying aspects of a genome sequencing project is the identification of the genes contained within it.These are of two types: those which encode tRNAs and those which produce proteins. After a general introduction on the properties of protein-encoding genes and the utility of the Basic Local Alignment Search Tool (BLASTX) to identify genes through homologs, a variety of tools are discussed by their creators. These include for genome annotation: GeneMark, Artemis, and BASys; and, for genome comparisons: Artemis Comparison Tool (ACT), Mauve, CoreGenes, and GeneOrder.

Affiliation(s): (4) Public Health Agency of Canada, Laboratory for Foodborne Diseases, Guelph, Ontario, Canada
(5) Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
(6) Department of Microbiology, Immunology Queen’s University, Kingston, Ontario, Canada
(7) Wallace H. Coulter Department of Biomedical Engineering and Division of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
(8) Wellcome Trust Genome Campus, Sulston Laboratories, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
(9) Wellcome Trust Genome Campus, Sulston Laboratories, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
(10) University of Wisconsin-Madison, Madison, WI, USA
(11) Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
(12) Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA, USA
(13) Department of Biological Sciences, Biological Sciences Centre, University of Alberta, Edmonton, Alberta, Canada
(14) Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA, USA
(15) National Microbiology Laboratory, Canadian Science Centre for Human and Animal Health, Winnipeg, Manitoba, Canada
(16) Department of Computing Science and Biological Sciences, National Institute for Nanotechnology, University of Alberta, Edmonton, Alberta, Canada

Book Title: Bacteriophages: Methods and Protocols, Volume 2 Molecular and Applied Aspects

Series: Methods in Molecular Biology | Volume: 502 | Pub. Date: Oct-28-2008 | Page Range: 57-89 | DOI: 10.1007/978-1-60327-565-1_6

Subject: Microbiology

Key Words: tRNA - transfer RNA - CDS - ORF - Software - Internet - ACT - Artemis Comparison Tool - Artemis - BASys - Blast - CoreGenes - Dotplot - frameshift - GeneMark - GeneOrder - intron - Mauve - Online Analysis Tools

References

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