Nucleic Acid and Protein Sequence Analysis and Bioinformatics

Abstract

Bioinformatics is the application of computer technology to the management and use of molecular biology and genetic information. It is based on computer science and statistics; the current focus is on probabilistic models to analyze biological sequences at the genome level and other “omics” levels (e.g. transcriptomics and proteomics data). The major challenge in bioinformatics is the accurate prediction and modelling of the genomewide RNA:DNA, RNA:RNA, protein:DNA, protein:RNA, and protein:protein interaction patterns in the entire range of cellular and extracellular environments. This achievement would lead to the solution of the principles of genome-structure organization, the identification of the transcription initiation and termination and the RNA splicing pattern of any primary transcript in any tissue and the precise prediction of the folding pathway of any protein, the formation of quaternary and quinary (intermolecular) structures, and the design of effective drugs. Here, we summarize the state of the art and the potential of sequence analysis. Since a single review cannot describe the ever-broadening subject that is genome analysis, we proceed by discussing methods for genome composition analysis, gene- and transcription-site identification, and analysis of repeats, and conclude with speculation on the future course of bioinformatics analyses. Keywords: Markov Process; Maximum Likelihood; Phylogenetic Inferences; Phylogenetic Tree