Kenta Nakai

Construction of a novel database containing aberrant splicing mutations of mammalian genes

To explore the rules for mammalian splice-site selection using a statistical approach, we constructed an aberrant splicing database containing an extensive collection of mammalian genetic disease mutations (90 genes, 209 mutations). From this database, we confirmed that: (1) more than 90% of mutations either destroy or create the splice-site consensus sequences; (2) the number of mutations mapped at individual residues in the splice-site regions roughly correlates to their conservation degrees in the consensus sequences; (3) about half of the observed aberrant splicing is exon skipping, while intron retention is rarely observed; (4) almost all of the major cryptic sites, activated by mutations, are mapped within an about 100-nt region from the authentic splice sites. Furthermore, we found that: (5) mutations are observed more frequently in the 5 splice-site region than in the 3 splice site region; (6) splice sites that are newly created by mutations are located upstream from the authentic splice sites. Hopefully, these observations will be used as rules for constructing a more effective prediction system of exon sequences.

The Membrane-proteins Encoded By Yeast Chromosome-III Genes

Examples are given for the analysis of the 68 putative membrane proteins encoded among the 170 predicted genes identified by the systematic sequencing of yeast chromosome III [(1992) Nature 357, 38‐56].

Gnome – an Internet-based sequence analysis tool

Gnome (GenomeNet Open Mail-service Environment) is a sequence analysis tool that enables an end-user to make use of several Internet- (mainly e-mail) based services with an easy-to-use graphical user interface. Users can conduct homology and motif searches, and database-entry retrieval against the latest databases by emitting search requests to and receiving their results form a search-server by e-mail. The search results are viewed and managed efficiently with this system. The Macintosh and X (Motif) versions of the Gnome client and the UNIX version of the Gnome server are available to academic users free of charge.