Systematic Classification of B. subtilis Genes and Construction of a Knowledge Base to Represent Functional Information

Bacills subtilis is a typical Gram-positive bacterium whose whole genomic sequence was determined. Before the genome sequencing was completed, we had constructed a B. subtilis genome database called BSORF [2]. This was not only a database of sequences, but also to store as many functional annotations as possible. Since the complete genome sequence of Bacillus subtilis had been determined [1], we also tried to classify whole ORF products in the viewpoint of functional categories. We started with the clustering of paralogous genes [3], and using the result of paralog clustering, we annotated transporter genes using other features like motifs and operon structures. To rearrange the resulting annotation, I constructed a knowledge base system using Java language. Since the main focus of B. subtilis and other microbial genome projects was shifted to the functional analysis, genome-informatics should also treat the functional information. Here I’ll present a framework for functional information representation that is suitable for WWW.