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BioCyc: Online Resource for Genome and Metabolic Pathway Analysis
Author(s) -
Caspi Ron,
Billington Richard,
Foerster Hartmut,
Fulcher Carol A.,
Keseler Ingrid,
Kothari Anamika,
Krummenacker Markus,
Latendresse Mario,
Mueller Lukas A.,
Ong Quang,
Paley Suzanne,
Subhraveti Pallavi,
Weaver Dan S.,
Karp Peter D.
Publication year - 2016
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.30.1_supplement.lb192
Subject(s) - genome , metabolic network , organism , metabolic pathway , computational biology , genome browser , gene , model organism , annotation , computer science , genomics , biology , genetics
BioCyc.org is a genomic resource that contains more than 7600 Pathway/Genome Databases (PGDBs) for organisms whose genomes have been completely sequenced. Although most PGDBs are bacterial, PGDBs exist for key experimental organisms, including humans (HumanCyc), yeast (YeastCyc), and Arabidopsis (AraCyc). Each BioCyc database integrates the genome sequence of one organism with its predicted metabolic network, including metabolic pathways, reactions, and chemical compounds, all presented via a user‐friendly graphical interface. The BioCyc databases contain additional computed information such as predicted operons and candidate enzymes for catalyzing predicted enzymatic steps that have no assigned enzymes in the genome annotation. The BioCyc.org website enables users to perform many types of searches and data analyses online. Analysis tools include comparisons of pathways and genomes among multiple organisms, alignment of orthologous genes in a multi‐genome browser, and searching for minimal‐cost metabolic network routes that connect two substrates. Tools are also provided for visualizing omics data – such as metabolomics and gene expression data – on individual pathway diagrams, on personalized groups of multiple pathway diagrams called pathway collages, and on diagrams depicting the full metabolic network of an organism. A powerful tool in BioCyc is Smart Tables, which are user‐defined groups of metabolites or genes that can be transformed easily into other types of objects, analyzed, saved in a BioCyc account, and shared with other users. All BioCyc databases save one were created computationally using MetaCyc as a reference. MetaCyc (MetaCyc.org) is a comprehensive manually‐curated metabolic database whose contents are derived from experimentally studies. It currently contains more than 2,400 experimentally determined metabolic pathways from more than 2,700 organisms, curated from more than 47,800 scientific publications. It also contains extensive information on metabolic enzymes, reactions, and substrates. The BioCyc databases can be accessed through the BioCyc.org web site and can be downloaded. In addition, the Pathway Tools software can be downloaded and installed locally to create BioCyc‐like databases for more genomes, curate existing databases, or perform additional analyses that are not available online. Support or Funding Information National Institute of General Medical Sciences of the National Institutes of Health (NIH) [GM080746, GM077678, GM75742].