Comparative genomics using data mining tools.
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 were Methanococcus jannaschii, Haemophilus influenzae and Saccharomyces 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 whereas S. 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
Nandi
Tannistha
T
Functional Genomics Unit, Centre for Biochemical Technology, Mall Road, Delhi 110 007, India.
B-Rao
Chandrika
C
Ramachandran
Srinivasan
S
D019843:Archaeal Proteins / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D019295:Computational Biology; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D016681:Genome, Fungal; D023281:Genomics; D006193:Haemophilus influenzae / Q000235:genetics*; D006801:Humans; D017017:Methanococcus / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D029701:Saccharomyces cerevisiae Proteins