Bioinformatics tools provided by the GenomeNet

These tools or the interfaces have been developed by the GenomeNet, except the core programs for the sequence analysis.

BLAST FASTA	Sequence similarity search	Altschul et al. (1997) Pearson and Lipman (1988)
MOTIF	Sequence motif search
CLUSTALW MAFFT PRRN	Multiple sequence alignment	Thompson et al. (1994) Kato and Standley (2013) Gotoh (1982)
TREE	Phylogeny

ViPTree	The Viral Proteomic Tree server	Nishimura et al. (2017)
KAAS	Automatic genome annotation (KO assignment) and pathway/brite mapping	Moriya et al. (2007)
MAPLE	Metabolic and physiological potential evaluator	Takami et al. (2012)
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) / Kotera et al. (2012)
DINIES	Drug-target interaction network inference	Yamanishi et al. (2010)

SIMCOMP	Chemical structure similarity search	Hattori et al. (2003) / (2010)
SUBCOMP	Chemical substructure search	Hattori et al. (2010)
KCaM	Glycan structure similarity search	Aoki et al. (2004)
GECS	Glycan structure prediction from microarray data	Kawano et al. (2005) Suga et al. (2007)
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)
PathComp	Possible reaction path computation	Goto et al. (1997)
PathSearch	Similar reaction path search

Bioinformatics tools provided by the Kyoto University Bioinformatics Center

The following tools have also been developed by the Kyoto University Bioinformatics Center. They are maintained by the individual laboratories.

EnuMol	Enumerating Molecular Structures	Shimizu et al. (2011)
MIMOX	A web tool for phage display analysis	Huang et al. (2006)
HSEpred	predict Half-Sphere Exposure from protein sequences	Song et al. (2008)
PRORATE	prediction of protein folding rates	Song et al. (2010)
SLPFA	Subcellular Location Prediction with Frequency and Alignment	Tamura & Akutsu (2007)
INTREPED	an interactive DNA repair prediction server	Brown & Akutsu (2009)
IPPI	Inferring Protein-Protein Interactions for YEAST	Hayashida et al. (2003)
PURE	A Pubmed article recommendation system based on content-based filtering	Yoneya & Mamitsuka (2007)

PLOC	Prediction of protein localization sites	Park & Kanehisa (2003)
TSEG	Prediction of membrane proteins	Kihara et al. (1998)
HAMSTER	Helpful Abstraction using Minimum Spanning Trees for Expression Relations	Wan et al. (2009)