KBase Narrative - Metabolically diverse Miscanthus x giganteus microbiome isolates with tremendous growth-promoting potential - Copy

Name: KBase Narrative - Metabolically diverse Miscanthus x giganteus microbiome isolates with tremendous growth-promoting potential - Copy
Published: Thu Mar 28 00:00:00 EDT 2024

Schirmer, Aaron; Whitham, Jason

doi:10.25982/175568.4/2329277

KBase Narrative - Metabolically diverse Miscanthus x giganteus microbiome isolates with tremendous growth-promoting potential - Copy

Dataset · Thu Mar 28 00:00:00 EDT 2024

DOI:https://doi.org/10.25982/175568.4/2329277· OSTI ID:2329277

^[1]; Whitham, Jason ^[2]

Northeastern Illinois University; Oak Ridge National Laboratory
North Carolina State University

This module analyzes the impact of fertilizer on the soil microbiome and attempts to identify isolates that could be used to make green fertilizers.

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Research Organization:: U.S. Department of Energy Systems Biology Knowledgebase

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI ID:: 2329277

Country of Publication:: United States

Language:: English

References (26)

KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Interactive metagenomic visualization in a Web browser Ondov, Brian D.; Bergman, Nicholas H.; Phillippy, Adam M. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-385	journal	September 2011
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
Identification, variation and transcription of pneumococcal repeat sequences Croucher, Nicholas J.; Vernikos, Georgios S.; Parkhill, Julian BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-120	journal	February 2011
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies Akhter, Sajia; Aziz, Ramy K.; Edwards, Robert A. Nucleic Acids Research, Vol. 40, Issue 16 https://doi.org/10.1093/nar/gks406	journal	May 2012
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Brettin, Thomas; Davis, James J.; Disz, Terry Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08365	journal	February 2015
Metagenome-assembled genome extraction and analysis from microbiomes using KBase Chivian, Dylan; Jungbluth, Sean P.; Dehal, Paramvir S. Nature Protocols, Vol. 18, Issue 1 https://doi.org/10.1038/s41596-022-00747-x	journal	November 2022
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Translational recoding in archaea Cobucci-Ponzano, Beatrice; Rossi, Mosè; Moracci, Marco Extremophiles, Vol. 16, Issue 6 https://doi.org/10.1007/s00792-012-0482-8	journal	September 2012
SMART: recent updates, new developments and status in 2015 Letunic, Ivica; Doerks, Tobias; Bork, Peer Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku949	journal	October 2014
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes Selengut, J. D.; Haft, D. H.; Davidsen, T. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl1043	journal	January 2007
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
The Pfam protein families database: towards a more sustainable future Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1344	journal	December 2015
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome Nayfach, Stephen; Pollard, Katherine S. Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0611-7	journal	March 2015
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
BLAT---The BLAST-Like Alignment Tool Kent, W. J. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.229202	journal	March 2002
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
20 years of the SMART protein domain annotation resource Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx922	journal	October 2017
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
FIGfams: yet another set of protein families Meyer, Folker; Overbeek, Ross; Rodriguez, Alex Nucleic Acids Research, Vol. 37, Issue 20 https://doi.org/10.1093/nar/gkp698	journal	September 2009
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures Marchler-Bauer, Aron; Bo, Yu; Han, Lianyi Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1129	journal	November 2016
TIGRFAMs and Genome Properties in 2013 Haft, Daniel H.; Selengut, Jeremy D.; Richter, Roland A. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1234	journal	November 2012
A Genomic Perspective on Protein Families Tatusov, R. L. Science, Vol. 278, Issue 5338 https://doi.org/10.1126/science.278.5338.631	journal	October 1997

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