Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package
作者： Byeonghyeok Park , Min-Jeong Baek , Byoungnam Min , In-Geol Choi
关键词:
摘要: … a light and portable prokaryotic genome annotation pipeline for … ‘‘P-CAPS’’ (Prokaryotic Contig Annotation Pipeline Server). The … The annotations from P-CAPS and Prokka showed near …
elsevier.com
sci-hub.se 参考文章(10)
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
Grzegorz M. Boratyn, Christiam Camacho, Peter S. Cooper, George Coulouris, Amelia Fong, Ning Ma, Thomas L. Madden, Wayne T. Matten, Scott D. McGinnis, Yuri Merezhuk, Yan Raytselis, Eric W. Sayers, Tao Tao, Jian Ye, Irena Zaretskaya, BLAST: a more efficient report with usability improvements Nucleic Acids Research. ,vol. 41, pp. 29- 33 ,(2013) , 10.1093/NAR/GKT282
T. Seemann, Prokka: Rapid Prokaryotic Genome Annotation Bioinformatics. ,vol. 30, pp. 2068- 2069 ,(2014) , 10.1093/BIOINFORMATICS/BTU153
P. Jones, D. Binns, H.-Y. Chang, M. Fraser, W. Li, C. McAnulla, H. McWilliam, J. Maslen, A. Mitchell, G. Nuka, S. Pesseat, A. F. Quinn, A. Sangrador-Vegas, M. Scheremetjew, S.-Y. Yong, R. Lopez, S. Hunter, InterProScan 5: genome-scale protein function classification Bioinformatics. ,vol. 30, pp. 1236- 1240 ,(2014) , 10.1093/BIOINFORMATICS/BTU031
John Besemer, Alexandre Lomsadze, Mark Borodovsky, GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions Nucleic Acids Research. ,vol. 29, pp. 2607- 2618 ,(2001) , 10.1093/NAR/29.12.2607
Doug Hyatt, Gwo-Liang Chen, Philip F LoCascio, Miriam L Land, Frank W Larimer, Loren J Hauser, Prodigal: prokaryotic gene recognition and translation initiation site identification BMC Bioinformatics. ,vol. 11, pp. 119- 119 ,(2010) , 10.1186/1471-2105-11-119
Todd M. Lowe, Sean R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research. ,vol. 25, pp. 955- 964 ,(1997) , 10.1093/NAR/25.5.0955
Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, Evgeny M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics. ,vol. 31, pp. 3210- 3212 ,(2015) , 10.1093/BIOINFORMATICS/BTV351
M. E. Skinner, A. V. Uzilov, L. D. Stein, C. J. Mungall, I. H. Holmes, JBrowse: a next-generation genome browser. Genome Research. ,vol. 19, pp. 1630- 1638 ,(2009) , 10.1101/GR.094607.109