BioSystems., 47, 119-128 (1998)
Computation with the KEGG pathway database
Hiroyuki Ogata, Susumu Goto, Wataru Fujibuchi,
and
Minoru Kanehisa*
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
Abstract
We introduce and discuss a new computational approach towards prediction and
inference of biological functions from genomic sequences by making use of the
pathway data in KEGG. Because of its piecewise nature, the current approach of
predicting each gene function based on sequence similarity searches often fails to
reconstruct cellular functions with all necessary components. The pathway diagram in
KEGG, which may be considered a wiring diagram of molecules in biological systems,
can be utilized as a reference for functional reconstruction. KEGG also contains binary
relations that represent molecular interactions and relations and that can be utilized for
computing and comparing pathways.
Keywords: pathway reconstruction, pathway comparison, sequence analysis, gene
organization in the genome
*Corresponding author: Minoru Kanehisa
Fax: +81-774-38-3269
E-mail: kanehisa@kuicr.kyoto-u.ac.jp