Here we present a comprehensive software suite for sequence-based bioinformatics analysis of annotated cDNAs, including tools for the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative structure modeling of the product protein structure, identification of alternative splice forms, and comparative systems biology by metabolic pathway reconstruction. Therefore, the analyses implemented in the software system covers the levels of nucleotide sequence, codons, mRNA variants, amino acid sequence, protein structure, and metabolic pathway. Although the target unit is the cDNA, the system can be used for a variety of other data sets including EST, GSS, and complete genome data.

Software (Click here to download)

--- Click here for README file of the software. ---
The software is open source and freely available under the GNU General Public License version 2. Most software should work on the platforms where G-language Genome Analysis Environment works, and should work best on RedHat or Fedora Core Linux.

Additional data files
The following additional data files are available for the manuscript. Additional data file 1 contains a complete listing of 126 parameters used for interpretation of PCA of codon usage, with correlation coefficients between the parameters and the first 4 principal components calculated with human cDNA data. Additional data file 2 is a sample output of the metabolic pathway comparison tool, for a query of glycolysis in E.coli against glycolysis pathways of all organisms in KEGG. Additional data file 3 contains the PWM, graphs of calculated indices, and sequence logo output results of the detection of translation initiation signals using mouse cDNA data. Additional data file 4 is the PDB format file of a structure modeled from the human FLJ00094 gene. Additional data file 5 is the raw output of the metabolic pathway comparison tool, from a query of reconstructed E. coli K12 pathways against the E. coli K12 database of KEGG.
  • Additional data file 1
  • Additional data file 2
  • Additional data file 3
  • Additional data file 4
  • Additional data file 5

  • (C) 2005 Institute for Advanced Biosciences, Keio University