TREADS: Target Research for Anti-epileptic Drugs Using Data Science.

Context: Epilepsy is a common neurological disease and is classified into different types based on features such as the kind of seizure, age of onset, part of brain effected, etc. There are nearly 30 approved anti-epileptic drugs (AEDs) for treating different epilepsies and each drug targets proteins exhibiting a specific molecular mechanism of action. There are many genes, proteins, and microRNAs known to be associated with different epileptic disorders.

Identification of 3'-UTR single nucleotide variants and prediction of select protein imbalance in mesial temporal lobe epilepsy patients.

The genetic influence in epilepsy, characterized by unprovoked and recurrent seizures, is through variants in genes critical to brain development and function. We have carried out variant calling in Mesial Temporal Lobe Epilepsy (MTLE) patients by mapping the RNA-Seq data available at SRA, NCBI, USA onto human genome assembly hg-19. We have identified 1,75,641 SNVs in patient samples.

Master Blaster: an approach to sensitive identification of remotely related proteins.

Genome sequencing projects unearth sequences of all the protein sequences encoded in a genome. As the first step, homology detection is employed to obtain clues to structure and function of these proteins. However, high evolutionary divergence between homologous proteins challenges our ability to detect distant relationships.

Unity and diversity among viral kinases.

Viral kinases are known to undergo autophosphorylation and also phosphorylate viral and host substrates. Viral kinases have been implicated in various diseases and are also known to acquire host kinases for mimicking cellular functions and exhibit virulence. Although substantial analyses have been reported in the literature on diversity of viral kinases, there is a gap in the understanding of sequence and structural similarity among kinases from different classes of viruses.

Classification of Protein Kinases Influenced by Conservation of Substrate Binding Residues.

With the advent of genome sequencing projects in the recent past, several kinases have come to light as regulating different signaling pathways. These kinases are generally classified into different subfamilies based on their sequence similarity with members of known subfamilies of kinases. A functional association is then defined to the kinase based on the subfamily to which it has been characterized.

Motif detection in Arabidopsis: correlation with gene expression data.

The genes having similar expression profiles are considered to have common regulatory mechanisms and are controlled by the binding of transcription factors to the regulatory elements present in their upstream regions. The detection of cis-regulatory elements can help in further understanding of co-expression of genes. This paper deals with the detection of motifs in the upstream regions of genes involved in diurnal rhythms of Arabidopsis and also deals with the correlation of expression data with sequence information.

Accelerating comparative genomics using parallel computing.

In the past decade there has been an increase in the number of completely sequenced genomes due to the race of multibillion-dollar genome-sequencing projects. The enormous biological sequence data thus flooding into the sequence databases necessitates the development of efficient tools for comparative genome sequence analysis. The information deduced by such analysis has various applications viz.