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

Autor:	Shaffer M; Colorado State University, Fort Collins, CO, USA., Borton MA; Colorado State University, Fort Collins, CO, USA., Bolduc B; The Ohio State University, Columbus, OH, USA., Faria JP; Argonne National Laboratory, Lemont, IL, USA., Flynn RM; Colorado State University, Fort Collins, CO, USA., Ghadermazi P; Colorado State University, Fort Collins, CO, USA., Edirisinghe JN; Argonne National Laboratory, Lemont, IL, USA., Wood-Charlson EM; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Miller CS; University of Colorado Denver, Denver, CO, USA., Chan SHJ; Colorado State University, Fort Collins, CO, USA., Sullivan MB; The Ohio State University, Columbus, OH, USA., Henry CS; Argonne National Laboratory, Lemont, IL, USA., Wrighton KC; Colorado State University, Fort Collins, CO, USA.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2023 Apr 03; Vol. 39 (4).
DOI:	10.1093/bioinformatics/btad110
Abstrakt:	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. Availability and Implementation: For kb_DRAM users, the kb_DRAM apps on KBase can be found in the catalog at https://narrative.kbase.us/#catalog/modules/kb_DRAM. For kb_DRAM users, a tutorial workflow with all documentation is available at https://narrative.kbase.us/narrative/129480. For kb_DRAM developers, software is available at https://github.com/shafferm/kb_DRAM. (© The Author(s) 2023. Published by Oxford University Press.)
Databáze:	MEDLINE
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