RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
作者： Thomas Brettin , James J. Davis , Terry Disz , Robert A. Edwards , Svetlana Gerdes
DOI: 10.1038/SREP08365
关键词:
摘要: The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes RNA) annotating their functions. Recently, order make more useful research tool keep pace with advancements bioinformatics, it has become desirable build version of that is both customizable extensible. In this paper, we describe the kit (RASTtk), modular enables researchers custom pipelines. RASTtk offers choice as well ability add an job. also accommodates batch submission genomes customize protocols submissions. This first major restructuring since its inception.
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Jordan Matthew Utley, R-FAP: Rapid Functional Annotation of Prokaryotes Using Taxon-specific Pan-genomes and 10-mer Peptides ,(2014)
Rotem Sorek, Victor Kunin, Philip Hugenholtz, CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea Nature Reviews Microbiology. ,vol. 6, pp. 181- 186 ,(2008) , 10.1038/NRMICRO1793
Chu Qin, Cheng Zhang, Feng Zhu, Feng Xu, Shang Ying Chen, Peng Zhang, Ying Hong Li, Sheng Yong Yang, Yu Quan Wei, Lin Tao, Yu Zong Chen, Therapeutic target database update 2014: a resource for targeted therapeutics Nucleic Acids Research. ,vol. 42, pp. 1118- 1123 ,(2014) , 10.1093/NAR/GKT1129
Folker Meyer, Ross Overbeek, Alex Rodriguez, FIGfams: yet another set of protein families Nucleic Acids Research. ,vol. 37, pp. 6643- 6654 ,(2009) , 10.1093/NAR/GKP698
Erika Check Hayden, Technology: The $1,000 genome Nature. ,vol. 507, pp. 294- 295 ,(2014) , 10.1038/507294A
James J. Davis, Gary J. Olsen, Ross Overbeek, Veronika Vonstein, Fangfang Xia, In search of genome annotation consistency: solid gene clusters and how to use them 3 Biotech. ,vol. 4, pp. 331- 335 ,(2014) , 10.1007/S13205-013-0152-2
Alice R. Wattam, David Abraham, Oral Dalay, Terry L. Disz, Timothy Driscoll, Joseph L. Gabbard, Joseph J. Gillespie, Roger Gough, Deborah Hix, Ronald Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Robert Olson, Ross Overbeek, Gordon D. Pusch, Maulik Shukla, Julie Schulman, Rick L. Stevens, Daniel E. Sullivan, Veronika Vonstein, Andrew Warren, Rebecca Will, Meredith J.C. Wilson, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Bruno W. Sobral, PATRIC, the bacterial bioinformatics database and analysis resource Nucleic Acids Research. ,vol. 42, pp. 581- 591 ,(2014) , 10.1093/NAR/GKT1099
Prashant Mali, Luhan Yang, Kevin M Esvelt, John Aach, Marc Guell, James E DiCarlo, Julie E Norville, George M Church, RNA-Guided Human Genome Engineering via Cas9 Science. ,vol. 339, pp. 823- 826 ,(2013) , 10.1126/SCIENCE.1232033
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
B. Liu, M. Pop, ARDB—Antibiotic Resistance Genes Database Nucleic Acids Research. ,vol. 37, pp. 443- 447 ,(2009) , 10.1093/NAR/GKN656