• Chandrika B-Rao

      Articles written in Journal of Biosciences

    • Reconstruction of phylogenetic relationships

      Chandrika B-Rao Kshitish C Majumdar

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      In this paper, we provide an introductory overview to the field of phylogenetic analysis, which has wide applications in modern biology.

    • Comparative genomics using data mining tools

      Tannistha Nandi Chandrika B-Rao Srinivasan Ramachandran

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      We have analysed the genomes of representatives of three kingdoms of life, namely, archaea, eubacteria and eukaryota using data mining tools based on compositional analyses of the protein sequences. The representatives chosen in this analysis wereMethanococcus jannaschii, Haemophilus influenzae andSaccharomyces cerevisiae. We have identified the common and different features between the three genomes in the protein evolution patterns.M. jannaschii has been seen to have a greater number of proteins with more charged amino acids whereasS. cerevisiae has been observed to have a greater number of hydrophilic proteins. Despite the differences in intrinsic compositional characteristics between the proteins from the different genomes we have also identified certain common characteristics. We have carried out exploratory Principal Component Analysis of the multivariate data on the proteins of each organism in an effort to classify the proteins into clusters. Interestingly, we found that most of the proteins in each organism cluster closely together, but there are a few ‘outliers’. We focus on the outliers for the functional investigations, which may aid in revealing any unique features of the biology of the respective organisms.

    • Bhattacharyya’s distance measure as a precursor of genetic distance measures

      Aparna Chattopadhyay Asis Kumar Chattopadhyay Chandrika B-Rao

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      In Population Genetics, two populations are distinguished from each other on the basis of the differences in the distributions of the alleles at the locus or loci under consideration. These differences are measured by a “genetic distance” between the two populations (not to be confused with genetic distance between two loci, which is based on recombination fractions) and they play a major role in inferences at the population level. Several measures of genetic distance have been proposed by different authors (Sanghvi 1953; Cavalli-Sforza and Edwards 1967; Jukes and Cantor 1969; Nei 1972; Kimura 1980; Reynoldset al 1983; reviews in Felsenstein 1991; Nei and Kumar 2000). Most of these measures are actually dissimilarity measures and not mathematically true distance measures (B-Rao and Majumdar 1999). Independently, and much before the geneticists, statisticians too were concerned with the idea of distinguishing between two (statistical) populations. In order to discriminate between two populations on the basis of one or more characters, divergence measures like “Mahalanobis’D2 statistic” or “Mahalanobis’ generalized distance” (1936) and “Bhattacharyya’s distance” (1943, 1946), Kullback-Leibler’s divergence measure (1951) etc. have been proposed by statisticians. Mukherjee and Chattopadhyaya (1986) have mentioned measures based on distances, association between two attributes and discrimination function. There are similarities between the distance measures defined by applied scientists and by theoreticians. Felsenstein (1985) shows that three of the allele frequency-based genetic distance measures were anticipated by Bhattacharyya (1946). Nei and Takezaki (1994) have also studied the effectiveness of several genetic distance measures in the context of phylogenetic analysis, including Bhattacharyya’s distance measure.

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