The BioCyc collection of microbial genomes and metabolic pathways

Abstract

BioCyc.org 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.

Keywords: genome databases; metabolic pathway databases; microbial genome databases.

Figure 1

Processing steps involved in generating the BioCyc DBs. Recently added steps are shown in bold. No relative ordering is implied between the steps along the top and the steps along the bottom.

Figure 2

SmartTable showing essential genes and their metabolic pathways in C. difficile 630.

Figure 3

Escherichia coli gene expression data from an anaerobic to aerobic transition (Gene expression omnibus id GDS2364) superimposed on a pathway collage. Each horizontal row of squares indicates the expression levels of one gene across the four oxygen levels depicted, where the leftmost square is anaerobic and the rightmost square is the highest oxygen concentration. Blue and purple indicate low expression, gray indicates intermediate expression and orange indicates high expression.