Databases and Systems

(2) Java applets to search, compare, and handle genome maps
(3) CGI scripts to search and handle hierarchical texts
(4) CGI scripts to search and color HTML tables
(5) a suite of software tools for network comparison and pathway reconstruction
The major types of network data shown in Table 2 can be searched in different
ways as summarized in Table 4. These capabilities effectively make it possible to
perform network comparisons. In fact, it is the main purpose of the KEGG system to
treat a network or a subnetwork as a unit. Of course, a KEGG query can be made
with a single element against a network, but it is better made with multiple elements
against a network to see if, for example, a correct subnetwork (functional unit) is
formed.
Table 4. Searching elements in the KEGG network data.
Actually, the traditional sequence alignment is a network comparison problem
with relatively stringent conditions; namely, the network is one-dimensional and the
order of network elements (amino acids or nucleotides) cannot be changed. The
network comparison in KEGG is a more general problem. By comparing a genome
and a pathway we wish to identify localized genes in the genome, for example, genes
in an operon, that function in a closely related positions in the biochemical pathway.
By comparing a sequence similarity network (neighbor) and a pathway we wish to
identify duplicated genes forming successive steps in the biochemical pathway. A
general algorithm to compare different types of networks was developed (H. Ogata,
W. Fujibuchi, and M. Kanehisa, manuscript in preparation), has been used in
organizing ortholog group tables (see below), and is provided as software tools in the
KEGG system.
Relational database system
An entry of GENES contains, among others, amino acid and nucleotide sequence
information that is extracted from the GenBank database, but the description of the
gene can be different from GenBank because the functional assignment is reexamined
by KEGG. To help this process and to manage updates of the GENES
database we use the Sybase relational database system. The system, which is linked
to a Web-based gene annotation tool, is limited to internal use.
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