The combination of full-scale genomic sequencing with high throughput expression analysis provides a new and largely unexploited basis for in silico functional genomics. Recent break through developments in locating and analyzing promoters now allow extending functional genomics in silico far beyond identification of protein sequences into the complex regulatory structures and mechanisms of the...

The present study deals with the identification, isolation and in silico characterization of gene encoding geraniol dehydrogenase from Ocimum americanum. Mature leaves of plants have a higher degree of secondary metabolites that hampers the nucleic acid isolation, PCR amplification and other downstream reactions. The DNA isolation from mature leaves of O. americanum is described here which invo...

An increasing number of studies have demonstrated the effectiveness of flagellin (FliC) as an adjuvant. In this study, FliC(s) from Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa, and Escherichia coli were compared. In silico studies were designed to determine physicochemical parameters of FliC from different bacteria. The fliC gene corresponding to best model was amplified, cl...

Deregulated immune response to gut microflora in genetically predisposed individuals is typical for inflammatory bowel diseases. It is reasonable to assume that genetic association with the disease will be more pronounced in subjects with early onset than adult onset. The nucleotide-binding oligomerization domain containing-2 gene, commonly involved in multifactorial risk of Crohn's disease, an...

UNLABELLED : Cinnamoyl CoA reductase (CCR) carries out the first committed step in monolignol biosynthesis and acts as a first regulatory point in lignin formation. CCR shows multiple substrate specificity towards various cinnamoyl CoA esters. Here, in Silico mutagenesis studies of active site residues of Ll-CCRH1 were carried out. Homology modeling based modeled 3D structure of Ll-CCRH1 was us...

In silico genome analysis enables systematic identification of potential antigens within a pathogen. Of primary importance is the accuracy of computer algorithms used for antigen prediction. Most bioinformatics tools are based on sequence alignment and are not able to predict truly novel antigenic proteins which lack similarity to existing antigens or which encode antigenicity in a cryptic mann...

The chemical space based on physicochemical properties and structural features of a diverse group of natural products with reported in vitro activity against different Mycobacterium tuberculosis strains is investigated using in silico tools. This is compared to the chemical space occupied by drugs currently recommended for the treatment of various forms of tuberculosis as well as compounds in p...

Tracking gliomas dynamics on MRI has became more and more important for therapeutic management. Powerful computational tools have been recently developed in this context enabling in silico growth on a virtual brain that can be matched with real 3D segmented evolution through registration between atlases and patient brain MRI data. In this paper, we provide an extensive review of existing algori...

Uridine-cytidine kinase 2 is implicated in uncontrolled proliferation of abnormal cells and it is a hallmark of cancer, therefore, there is need for effective inhibitors of this key enzyme. In this study, we employed the used of in silico studies to find effective UCK2 inhibitors of natural origin using bioinformatics tools. An in vitro kinase assay was established by measuring the amount of AD...

Summary Whole genome sequencing (WGS) is being adopted in public health for improved surveillance and outbreak analysis. In public health, subtyping has been used to infer phenotypes and distinguish bacterial strain groups. In silico tools that predict subtypes from sequences data are needed to transition historical data to WGS-based protocols. Phylotyper is a novel solution for in silico subty...