Genomic characterization of six novel Bacillus pumilus bacteriophages
Laura Lorenz,Bridget Lins,Jonathan M. Barrett,Andrew Montgomery,Stephanie E. Trapani,Anne Schindler,Gail E. Christie,Steven G. Cresawn,Larissa K. Temple +8 more
Reads0
Chats0
TLDR
Despite isolation over wide geographic and temporal space, the six cluster BpA phages share most of their 23 functionally annotated protein features and show a high degree of sequence similarity, which is unique among phages of the Bacillus genera.About:
This article is published in Virology.The article was published on 2013-09-01 and is currently open access. It has received 34 citations till now. The article focuses on the topics: Bacillus pumilus & Bacteriophage.read more
Citations
More filters
Journal ArticleDOI
A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students
Tuajuanda C. Jordan,Sandra H. Burnett,Susan Carson,Steven M. Caruso,Kari Clase,Randall J. DeJong,John J. Dennehy,Dee R. Denver,David Dunbar,Sarah C. R. Elgin,Ann M. Findley,Chris R. Gissendanner,Urszula Golebiewska,Nancy Guild,Grant A. Hartzog,Wendy H. Grillo,Gail P. Hollowell,Lee E. Hughes,Allison Johnson,Rodney A. King,Lynn O. Lewis,Wei Li,Frank Rosenzweig,Michael R. Rubin,Margaret S. Saha,James Sandoz,Christopher D. Shaffer,Barbara J. Taylor,Larissa K. Temple,Edwin Vazquez,Vassie C. Ware,Lucia P. Barker,Kevin W. Bradley,Deborah Jacobs-Sera,Welkin H. Pope,Daniel A. Russell,Steven G. Cresawn,David Lopatto,Cheryl Bailey,Graham F. Hatfull +39 more
TL;DR: A general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics is developed, showing that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence inScience, technology, engineering, and mathematics (STEM) disciplines.
Journal ArticleDOI
Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies
TL;DR: Modifications to the phage comparative genomics software program, Phamerator, are described, public access to the code is provided, and instructions for creating custom PhamerATOR databases are included for creating databases with individually selected genomes.
Journal ArticleDOI
Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity.
TL;DR: This analysis provides a basis for understanding and characterizing Bacillus phages and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria.
Journal ArticleDOI
Integration of genomic and proteomic analyses in the classification of the Siphoviridae family
Evelien M. Adriaenssens,Robert P. Edwards,John H. E. Nash,Padmanabhan Mahadevan,Donald Seto,Hans-Wolfgang Ackermann,Rob Lavigne,Andrew M. Kropinski,Andrew M. Kropinski +8 more
TL;DR: Using a variety of genomic and proteomic tools the authors have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae, and proposed 39 new genera, comprising 216 phage species, and added 62 species to two previously defined genera.
Journal ArticleDOI
Direct binding of ledipasvir to HCV NS5A: mechanism of resistance to an HCV antiviral agent.
Hyock Joo Kwon,Weimei Xing,Katie Chan,Anita Niedziela-Majka,Katherine M. Brendza,Thorsten A. Kirschberg,Kato Darryl,John O. Link,Guofeng Cheng,Xiaohong Liu,Roman Sakowicz +10 more
TL;DR: The current study shows that ledipasvir inhibits NS5A through direct binding and that resistance to ledip asvir is the result of a reduction in binding affinity to NS 5A mutants.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
NIH Image to ImageJ: 25 years of image analysis
TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Journal ArticleDOI
Clustal W and Clustal X version 2.0
Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Journal ArticleDOI
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
Fabian Sievers,Andreas Wilm,David Dineen,Toby J. Gibson,Kevin Karplus,Weizhong Li,Rodrigo Lopez,Hamish McWilliam,Michael Remmert,Johannes Söding,Julie D. Thompson,Desmond G. Higgins +11 more
TL;DR: A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality.
Journal ArticleDOI
Probability-based protein identification by searching sequence databases using mass spectrometry data.
TL;DR: A new computer program, Mascot, is presented, which integrates all three types of search for protein identification by searching a sequence database using mass spectrometry data, and the scoring algorithm is probability based.
Related Papers (5)
Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size.
Graham F. Hatfull,Deborah Jacobs-Sera,Jeffrey G. Lawrence,Welkin H. Pope,Daniel A. Russell,Ching-Chung Ko,Rebecca J. Weber,Manisha C. Patel,Katherine L. Germane,Robert H. Edgar,Natasha N. Hoyte,Charles A. Bowman,Anthony T. Tantoco,Elizabeth C. Paladin,Marlana S. Myers,Alexis L. Smith,Molly S. Grace,Thuy T. Pham,Matthew B. O'Brien,Amy M. Vogelsberger,Andrew J. Hryckowian,Jessica L. Wynalek,Helen Donis-Keller,Matt W. Bogel,Craig L. Peebles,Steven G. Cresawn,Roger W. Hendrix +26 more