kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

Shaffer, Michael; Borton, Mikayla A.; Bolduc, Ben; Faria, José P.; Flynn, Rory M.; Ghadermazi, Parsa; Edirisinghe, Janaka N.; Wood-Charlson, Elisha M.; Miller, Christopher S; Chan, Siu Hung Joshua; Sullivan, Matthew B.; Henry, Christopher S.; Wrighton, Kelly C.

doi:10.1093/bioinformatics/btad110

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

Journal Article · Wed Mar 01 00:00:00 EST 2023 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btad110· OSTI ID:1968059

^[1]; Borton, Mikayla A. ^[1]; Bolduc, Ben ^[2]; Faria, José P. ^[3]; Flynn, Rory M. ^[1]; Ghadermazi, Parsa ^[1]; Edirisinghe, Janaka N. ^[3]; Wood-Charlson, Elisha M. ^[4]; ^[5]; ^[1]; ^[2]; Henry, Christopher S. ^[3]; ^[1]

Colorado State University, Fort Collins, CO (United States)
The Ohio State University, Columbus, OH (United States)
Argonne National Laboratory (ANL), Argonne, IL (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
University of Colorado Denver , Denver, CO, USA

Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States); Colorado State University, Fort Collins, CO (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); University of Colorado, Denver, CO (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-06CH11357; SC0019746; SC0021350; SC0023084

OSTI ID:: 1968059

Alternate ID(s):: OSTI ID: 2008020
OSTI ID: 1985299
OSTI ID: 3012450

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 4 Vol. 39; ISSN 1367-4811

Publisher:: Oxford University Press (OUP)Copyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
KBase
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kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

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