ChemGenome 1.1

Home|Genome Analysis Software

ChemGenome is a physico-chemical method [1] which accepts DNA sequence in FASTA format and characterizes it as gene or nongene based on hydrogen bonding energy, stacking energy and groove potentials for each trinucleotide (codon). Read more about Genome Analysis

Agrobacterium tumefaciens (NC_003304) Wolinella succinogenes (NC_005090) Rhodopseudomonas palustris (NC_005296) Bordetella bronchiseptica (NC_002927) Clostridium acetobutylicium (NC_003030) Bordetella pertusis (NC_002929)
Above is a pictorial representation of the separation of genes(blue) from non-genes(red).

ChemGenome is ab initio in nature and has been tested on 294786 experimentally verified genes in 331 prokaryotic genomes. The observed average sensitivity, specificity & correlation-coefficient are found to be 96.9% (min: 90%, max: 100%), 86.0% & 85.0% respectively. Preliminary studies on eukaryotic genomes show that the model successfully separates the exonic regions from the non-coding regions.A software for whole genome analysis is available at

Please specify the E-mail id :   
Insert the Nucleotide sequence (in FASTA format)* :    Help

Please note before using the tool
  • The tool takes DNA sequence in FASTA format as input file.
  • Browse to select the input file and upload.
  • The input file can contain multiple sequences, each sequence being in FASTA format.
  • For multiple sequences, please specify the E-mail address or wait for a few minutes to get the on-line result.
  • Click on Submit to get the result
  • For further information, please see the Help file.

Suggestions and Comments
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[1] "A Phenomenological model for predicting melting temperatures of DNA sequences" Khandelwal G.,and Jayaram B.,PLoS One ,2010, 5(8), e12433.
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[2] "Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations", Singhal P., Jayaram B., Dixit S. B. and Beveridge D. L., Biophys J., 2008, 94, 11, 4173-4183.
Read Paper

[3] "Decoding the design principles of amino acids and the chemical logic of protein sequences", Jayaram B., Nature Precedings, 2008.
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[4] "A Physico-Chemical model for analyzing DNA sequences", Dutta S., Singhal P., Agrawal P., Tomer R., Kritee, Khurana E. and Jayaram B., J. Chem. Inf. Mod., 2006, 46(1), 78-85.
Read Abstract

[5] "Beyond the Wobble : The rule of conjugates", Jayaram B., Journal of Mol. Evol., 1997, 45, 704.
Read Paper

Copyright 2004-2016, Prof B. Jayaram & Co-workers
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