Chanchal K. Mitra

Learn More
We have studied the core promoter region in five sets of promoter sequences by calculating the average mutual information content H (relative entropy). We have used specially constructed substitution matrices to calculate mono and dinucleotide replacements in a given block of aligned sequences. These substitution matrices use log-odds form of scores, which(More)
The transcription start site (TSS) region shows greater variability compared with other promoter elements. We are interested to search for its variability by using information content as a measure. We note in this study that the variability is significant in the block of 5 nucleotides (nt) surrounding the TSS region compared with the block of 15 nt. This(More)
The information content (relative entropy) of transcription factor binding sites (TFBS) is used to classify the transcription factors (TFs). The TF classes are clustered based on the TFBS clustering using information content. Any TF belonging to the TF class cluster has a chance of binding to any TFBS of the clustered group. Thus, out of the 41 TFBS (in(More)
We present here the results obtained by applying several different methods to quantitatively measure regularities in protein sequences based on pair-preferences. We have studied the distribution of amino acid residues, singly as well as in pairs in a large data base and have attempted this task. We confirmed the existence of well-defined pair-preferences in(More)
We have carried out a comparative analysis of the sub-sequences of size six| ten at the (donor| acceptor) splice site regions of five different organisms. The frequency analysis of the unique sub-sequences at the donor and acceptor regions suggests that the distribution of their occurrence is approximately exponential. We have observed that the number of(More)
The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also show that it is possible to model the Krebs cycle with a(More)
We have studied the direct electrochemistry of horseradish peroxidase (HRP) coupled to gold nanoparticles (AuNP) using electrochemical techniques, which provide some insight in the application of biosensors as tools for diagnostics because HRP is widely used in clinical diagnostics kits. AuNP capped with (i) glutathione and (ii) lipoic acid was covalently(More)
Transcription factor binding sites (TFBS) are the specific DNA binding motifs that are recognized by a transcription factor, are typically short and are often degenerate. Sequence-specific binding of TFs to the DNA controls the gene expression regulation at transcription level. High throughput genome sequencing provides abundant data for TF binding(More)
MicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS) are(More)