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Computational ribonucleomics of heavy metal stress tolerant Bacillus sp. strain SJ-101 16SrRNA gene has led to the identification of a novel small non-coding RNA (sRNA) and promoter-like sequences within 3' region of the gene. Using RNAz web server, a 123 bp long functional sRNA with significant thermodynamic stability (Energy contribution: -25.2) and evolutionary conservation (structure conservation...
Probe design is the most important step for any microarray based assay. Accurate and efficient probe design and selection for the target sequence is critical in generating reliable and useful results. Several different approaches for probe design are reported in literature and an increasing number of bioinformatics tools are available for the same. However, based on the reported low accuracy, determining...
We introduce a method for comparing protein structures using the notion of residue contexts based on protein Calpha-atom backbones. The residue context is derived from the set of vectors from a given Calpha-atom to each other Calpha-atom in the molecule. A three-dimensional histogram is generated from these vectors, containing a relative distribution of the other Calpha-atoms for each Calpha-atom...
The analysis of gene expression time series obtained from microarray experiments can be effectively exploited to understand a wide range of biological phenomena from the homeostatic dynamics of cell cycle systems to the response of key genes to the onset of cancer or infectious disease. However, microarray data frequently contain a significant number of missing values making the application of common...
Discerning the similarity between two molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeted at understanding existing molecules as well as in guiding the synthesis...
Determining the number and location of disulfide bonds within a protein provide valuable insight into the protein's three-dimensional structure. Purely computational methods that predict the bonded cysteine pairings given a protein's primary structure have limitations in both prediction correctness and the number of bonds that can be predicted. Our approach utilizes tandem mass spectrometric (MS/MS)...
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