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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.

      Sequence analysis
BLAST
FASTA
Sequence similarity search
MOTIF Sequence motif search
CLUSTALW
MAFFT
PRRN
Multiple sequence alignment and phylogenetic analysis
      Genome analysis
OC Viewer Query interface for KEGG OC (KEGG Ortholog Cluster) Nakaya et al. (2013)
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

» More tools

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Kyoto University Bioinformatics Center