Chemgenome3.0
                         

Chemgenome is an ab-intio gene prediction software, which find genes in prokaryotic and viral genomes in all six reading frames and also gives the corresponding protein sequences. The methodology follows a physico-chemical approach and has been validated on 372 prokaryotic genomes. Read more about ChemGenome




Input File

OR paste Genome Sequence in FASTA format

Additional Parameters

Threshold Values :      Start Codon :   ATG   CTG    GTG   TTG

Method : DNA Protein Swissprot

E-mail ID : (Optional)

Threshold Value: If you have small genome you can specify lower threshold value to find smaller genes. If you have large genomes you can specify higher threshold value to weed out false positives

Start Codon: You can specify what should be the start codon with which you want to find genes.

Method :
DNA Space: The method takes complete or part of genome sequence of prokaryotic species in FASTA format as input file. It searches for genes based on physico-chemical properties of double-helical deoxyribonucleic acid (DNA).

Protein Space: The method takes the result generated from DNA space as input file and works as a filter based on stereochemical properties of protein sequences to reduce false positives.

Swissprot Space :The method takes the result generated from protein space as input file and calculates the standard deviation of a query nucleotide sequence (predicted gene sequence) with the swissprot proteins based on the frequency of occurrence of aminoacids. A threshold standard deviation is chosen to keep the false positives at minimum and precision at maximum.

There is no file size limitation for the genomes. We have tested on more than 5 MB genome file size available with us. If the program crashes on large genome size, more than 5 MB, please intimate us.

The computation may take 5-10 minutes depending upon the load on the web server and the size of the genome in the input file.

[Mirror] (http://chemgenome.wesleyan.edu)
References
[1] "A Phenomenological model for predicting melting temperatures of DNA sequences" Khandelwal G.,and Jayaram B.,PLoS One ,2010, 5(8), e12433.
Read Paper

[2] "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

[3] "Decoding the design principles of amino acids and the chemical logic of protein sequences", Jayaram B., Nature Precedings, 2008.
Read Paper

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

We will be glad to receive your suggestions and comments/feedback at scfbio@scfbio-iitd.res.in.

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