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Journal Article  January 1, 2017

The BioCyc collection of microbial genomes and metabolic pathways

SRI Authors Peter Karp, Mario Latendresse, Manish Kothari



Karp, P.D., Billington, R., Caspi, R., Fulcher, C.A., Latendresse, M., Kothari, A., Keseler, I.M., Krummenacker, M., Midford, P.E., Ong, Q., Ong, W.K., Paley, S.M., & Subhraveti, P. (2017). The BioCyc collection of microbial genomes and metabolic pathways. Briefings in Bioinformatics. 1-9. DOI: 10.1093/bib/bbx085

Abstract is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer’s assistance.

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