Bioinformatics Tools

The bioinformatics tools in the following three categories are available at GenomeNet. Except the standard programs for sequence similarity search and multiple sequence alignment, the tools have been developed by the Kyoto University Bioinformatics Center.

BLAST FASTA	Sequence similarity search
MOTIF	Sequence motif search
CLUSTALW MAFFT PRRN	Multiple sequence alignment and phylogenetic analysis

KAAS	Automatic genome annotation (KO assignment) and pathway/brite mapping	Moriya et al. (2007)
EGassembler	Automatic generation of consensus contigs from a set of ESTs	Masoudi-Nejad et al. (2006)
GENIES	Gene network prediction by kernel-based integration of heterogeneous data sets	Yamanishi et al. (2005)
GECS	Glycan structure prediction from microarray data	Kawano et al. (2005) Suga et al. (2007)

SIMCOMP	Chemical structure similarity search	Hattori et al. (2003)
SUBCOMP	Chemical substructure search
KCaM	Glycan structure similarity search	Aoki et al. (2004)
PathPred	Biodegradation/biosynthetic pathway prediction for a given compound	Moriya et al. (2010)
E-zyme	Enzymatic reaction prediction between chemical compounds	Kotera et al. (2004) Oh et al. (2007)