Annotate Metagenome Assembly and Re-annotate Metagenome with RASTtk - v1.073

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Annotate Metagenome Assembly and Re-annotate Metagenome with RASTtk (Rapid Annotations using Subsystems Technology toolkit).

This KBase App (Annotate Metagenome Assembly and Re-annotate Metagenome) uses components from the RAST (Rapid Annotations using Subsystems Technology) toolkit [1,2,3] to annotate prokaryotic assemblies or metagenome assemblies.

The release versions of the RASTtk component services used in this app are:

kb_seed: tag 20200922
kmer_annotation_figfam: tag 20200922
genome_annotation: tag 20200922

The Annotate Metagenome Assembly and Re-annotate Metagenome with RASTtk App takes an assembly or a metagenome assembly as an input, adds annotation and creates an Annotated Metagenome Assembly as an output object. This will make the annotations consistent with KBase genomes and prepare the metagenome for further analysis by other KBase Apps, especially the Metabolic Modeling Apps. An assembly is a FastA file imported as an Assembly object or is the output of one of the assembly apps in KBase

Team members who developed & deployed algorithm in KBase:

Thomas Brettin, James Davis, Terry Disz, Robert Edwards, Chris Henry, Gary Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon Pusch, Roman Sutormin, and Fangfang Xia. For questions, please contact us.

The authors of RAST request that if you use the results of this annotation in your work, please cite the first three listed publications:

Related Publications

[1] Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75 , https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-75
[2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226 , https://academic.oup.com/nar/article/42/D1/D206/1062536
[3] Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5. doi:10.1038/srep08365 , https://www.nature.com/articles/srep08365
[4] Kent WJ. BLAT The BLAST-Like Alignment Tool. Genome Res. 2002;12: 656 664. doi:10.1101/gr.229202 , https://genome.cshlp.org/content/12/4/656
[5] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402. doi:10.1093/nar/25.17.3389 ,
[6] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25: 955 964. , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/
[7] Cobucci-Ponzano B, Rossi M, Moracci M. Translational recoding in archaea. Extremophiles. 2012;16: 793 803. doi:10.1007/s00792-012-0482-8 , https://www.ncbi.nlm.nih.gov/pubmed/23015064
[8] Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009;37 6643-54. doi:10.1093/nar/gkp698. , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777423/
[9] van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol. 1996;34: 1176 1179. , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC228977/
[10] Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics. 2011;12: 120. doi:10.1186/1471-2164-12-120 , https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-120
[11] Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119 , https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119
[12] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23: 673 679. doi:10.1093/bioinformatics/btm009 , https://academic.oup.com/bioinformatics/article/23/6/673/419055
[13] Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012;40: e126. doi:10.1093/nar/gks406 , https://academic.oup.com/nar/article/40/16/e126/1027055

App Specification:

https://github.com/kbaseapps/RAST_SDK/tree/7171090d87fccc8b7ecf1a1d02398995dcc2dd45/ui/narrative/methods/annotate_metagenome

Module Commit: 7171090d87fccc8b7ecf1a1d02398995dcc2dd45