1. 1) ChemGenome 1.1 (GENE EVALUATOR): ChemGenome is a novel physico-chemical method for identifying protein coding regions on genomic DNA. The software tool accepts DNA sequence in FASTA format and characterizes it as a gene or non-gene based on hydrogen bonding energy, stacking energy and groove potentials for each trinucleotide (codon).

Ref.: S. Dutta, P. Singhal, P. Agrawal, R. Tomer, Kritee, E. Khurana, and B. Jayaram, "A Physico-chemical model for analyzing DNA sequences", J. Chem. Inf. Model., 2006, 46, 78-85. http://pubs.acs.org/doi/abs/10.1021/ci050119x

2. ChemGenome 2.0 (Gene Predictor): Chemgenome is an ab intio gene prediction software, which finds genes in prokaryotic genomes in all six reading frames. The methodology follows a physico-chemical approach and has been validated on 372 prokaryotic genomes.

Ref.: P. Singhal, B. Jayaram, S. B. Dixit and D. L. Beveridge, "Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations",Biophys J., 2008, 94,4173-4183. http://www.cell.com/biophysj/retrieve/pii/S0006349508700754

3. DNA CONVERTER: It accepts DNA sequence and translates it into all possible Amino Acid/Protein Sequences.

4. 4)Oligonucleotide Tm Predictor: It predicts the melting temperature of the given oligonucleotide at a particular salt concentration. The software is based on the hypothesis that hydrogen bonding an dstacking energy dictate the physical and thermal stability of DNA sequences. The user can provide the salt/Na ion concentration or it would take 0.16 M Na ion concentration as the default concentration. The maximum length of the sequence could be 70 bases.

Ref.: G. Khandelwal, and B. Jayaram, "A Phenomenological model for predicting melting temperatures of DNA sequences",PLoS One, 2010, 5, e12433. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012433

5. Tm Predictor for Longer Sequences: It predicts the melting temperature of the given DNA at a particular salt concentration. The user can provide the salt/Na ion concentration or it would take 0.16 M Na ion concentration as the default concentration. The minimum length of the sequence should be 70 bases. This tool has been demonstrated on entire genomes in the publications below.

Ref.: Garima Khandelwal, Jalaj Gupta and B. Jayaram, "DNA energetics based analyses suggest additional genes in prokaryotes", J. Bio Sc., 2012, 37, 433-444. http://link.springer.com/article/10.1007%2Fs12038-012-9221-7

6. Gene Predictor(ChemGenome 3.0): ChemGenome 3.0 is a gene prediction tool that takes a whole genome sequence or a part of the genome of a prokaryote or virus as input and predicts genes along with their coressponding protein sequences in all the six reading frames.

7.Visualization of DNA CURVES/CANAL

9. Onco-Regulon: Onco-Regulon is an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome.

Ref.: Akhilesh Mishra, Pradeep Pant, B. Jayaram, "Onco-Plus: an integrated database and computational protocol for discovery of lead molecules targeting unique DNA", J Mol Genet Med, 2018,12:92. DOI: 10.4172/1747-0862-C2-028

Akhilesh Mishra, Pradeep Pant, Nirotpal Mrinal and B. Jayaram, .A Computational protocol for the discovery of lead molecules targeting DNA unique to pathogens, Methods , 2017,131: 4-9. https://doi.org/10.1016/j.ymeth.2017.07.017

10. Pathogen Specific DNA Drug Finder (PSDDF): PSDDF is a computational protocol for identifying unique DNA sequence(s) in the pathogen which is absent in human and related non-pathogenic strains of the microbe. In order to use the unique sequence as drug target, the protocol, in the second step, uses virtual screening against a million compound library to identify candidate small molecules which can bind to these unique DNA targets in the pathogen only.