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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.

      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
      Genome analysis
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)
GECS Glycan structure prediction from microarray data Kawano et al. (2005)
Suga et al. (2007)
      Chemical analysis
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)
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)
The following services have been discontinued.
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)
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Kyoto University Bioinformatics Center