Prokka: Rapid Prokaryotic Genome Annotation

作者: T. Seemann

DOI: 10.1093/BIOINFORMATICS/BTU153

关键词: Data miningGenomeDNAPerlSequence analysisBacterial genome sizePan-genomeComputer scienceWhole genome sequencingMolecular Sequence AnnotationSequence assemblyContigComputational biologyGenome projectGenomics

摘要: … Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant …

参考文章(16)
Daniel H. Haft, Jeremy D. Selengut, Roland A. Richter, Derek Harkins, Malay K. Basu, Erin Beck, TIGRFAMs and Genome Properties in 2013 Nucleic Acids Research. ,vol. 41, pp. 387- 395 ,(2012) , 10.1093/NAR/GKS1234
E. J. Richardson, M. Watson, The automatic annotation of bacterial genomes Briefings in Bioinformatics. ,vol. 14, pp. 1- 12 ,(2013) , 10.1093/BIB/BBS007
Dean Laslett, Bjorn Canback, ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucleic Acids Research. ,vol. 32, pp. 11- 16 ,(2004) , 10.1093/NAR/GKH152
Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal, Folker Meyer, Gary J Olsen, Robert Olson, Andrei L Osterman, Ross A Overbeek, Leslie K McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko, The RAST Server: Rapid Annotations using Subsystems Technology BMC Genomics. ,vol. 9, pp. 75- 75 ,(2008) , 10.1186/1471-2164-9-75
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Stærfeldt, Torbjørn Rognes, David W. Ussery, RNAmmer: consistent and rapid annotation of ribosomal RNA genes Nucleic Acids Research. ,vol. 35, pp. 3100- 3108 ,(2007) , 10.1093/NAR/GKM160
R. R. Chaudhuri, N. J. Loman, L. A.S. Snyder, C. M. Bailey, D. J. Stekel, M. J. Pallen, xBASE2: a comprehensive resource for comparative bacterial genomics Nucleic Acids Research. ,vol. 36, pp. 543- 546 ,(2007) , 10.1093/NAR/GKM928
Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne, Henrik Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions Nature Methods. ,vol. 8, pp. 785- 786 ,(2011) , 10.1038/NMETH.1701
D. L. Kolbe, S. R. Eddy, Fast filtering for RNA homology search Bioinformatics. ,vol. 27, pp. 3102- 3109 ,(2011) , 10.1093/BIOINFORMATICS/BTR545
Marco Punta, Penny C Coggill, Ruth Y Eberhardt, Jaina Mistry, John Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik LL Sonnhammer, Sean R Eddy, Alex Bateman, Robert D Finn, None, The Pfam protein families database Nucleic Acids Research. ,vol. 30, pp. 276- 280 ,(2000) , 10.1093/NAR/GKR1065