This module contains the service code that implements the RASTtk genome annotation pipeline used by RAST and the BV-BRC genome annotation service
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
The original formulation of this code was to be run as a sychronous service via the KBase JSONRPC service mechanism. As such, the API for the service is defined in the GenomeAnnotation.spec file. Typical usage in BV-BRC is to directly invoke the invocation (see the p3_genome_annotation module); however in RAST and in the legacy genome annotation service still provided to users we use the synchronous form of this service.
In any event, the structure GenomeTO as defined in the specification file is used as the canonical definition of a genome object in the BV-BRC system. We provide the GenomeTypeObject Perl module for standardized access and update methods on genome objects.
Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC genomics 9, 75 (2008).
VIGOR4, https://github.com/JCVenterInstitute/VIGOR4.
McNair, K. et al. in Bacteriophages 231-238 (Springer, 2018).
McNair, K., Zhou, C., Dinsdale, E. A., Souza, B. & Edwards, R. A. PHANOTATE: a novel approach to gene identification in phage genomes. Bioinformatics 35, 4537-4542 (2019).
Overbeek, R. et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic acids research 33, 5691-5702 (2005).
Overbeek, R. et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). 42, D206-D214 (2013).
Davis, J. J. et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic acids research 48, D606-D612 (2020).
Brettin, T. et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific reports 5, 8365 (2015).
Mao, C. et al. Curation, integration and visualization of bacterial virulence factors in PATRIC. Bioinformatics 31, 252-258 (2015).
Ye, J., McGinnis, S. & Madden, T. L. BLAST: improvements for better sequence analysis. Nucleic acids research 34, W6-W9 (2006).
Croucher, N. J., Vernikos, G. S., Parkhill, J. & Bentley, S. D. Identification, variation and transcription of pneumococcal repeat sequences. BMC genomics 12, 1-13 (2011).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC bioinformatics 11, 1-11 (2010).
Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679 (2007).
Davis, J. J. et al. Antimicrobial resistance prediction in PATRIC and RAST. Scientific reports 6, 27930 (2016).
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome research 12, 656-664 (2002).
Johnson, M. et al. NCBI BLAST: a better web interface. Nucleic acids research 36, W5-W9 (2008).
Liu, B., Zheng, D., Jin, Q., Chen, L. & Yang, J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic acids research 47, D687-D692 (2019).
Xiang, Z. et al. VIOLIN: vaccine investigation and online information network. Nucleic acids research 36, D923-D928 (2007).
Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic acids research 48, D517-D525 (2020).
Liu, B. & Pop, M. ARDB—antibiotic resistance genes database. Nucleic acids research 37, D443-D447 (2009).
Antonopoulos, D. A. et al. PATRIC as a unique resource for studying antimicrobial resistance. Briefings in bioinformatics (2017).
Saier Jr, M. H. et al. The transporter classification database (TCDB): recent advances. Nucleic acids research 44, D372-D379 (2016).
Wishart, D. S. et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic acids research 46, D1074-D1082 (2018).
Chen, X., Ji, Z. L. & Chen, Y. Z. TTD: therapeutic target database. Nucleic acids research 30, 412-415 (2002).
Davis, J. J. et al. PATtyFams: Protein families for the microbial genomes in the PATRIC database. 7, 118 (2016).
Akhter, S., Aziz, R. K. & Edwards, R. A. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity-and composition-based strategies. Nucleic acids research 40, e126-e126 (2012).
Osawa, S., Jukes, T. H., Watanabe, K. & Muto, A. Recent evidence for evolution of the genetic code. Microbiological reviews 56, 229-264 (1992).
Rivest, R. & Dusse, S. (MIT Laboratory for Computer Science Cambridge, 1992).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome research 25, 1043-1055 (2015).