Bioinformatics approaches in studying microbial diversity

Abstract

Proper understanding of molecular sequences, identification and phylogenetics of microorganisms are very important in many branches of biological science. Generation of genomic DNA sequence data from different organisms including microbes requires the application of bioinformatics tools for their analysis. Bioinformatics tools including BLAST, multiple sequence alignment tools etc. are used to analyze nucleic acid and amino acid sequences for phylogenetic affiliation. The emerging fields of comparative genomics and phylogenomics require the substantial knowledge and understanding of computational methods to handle the large scale data involved. The introduction of comparative rRNA sequence analysis represents a major milestone in the history of microbiology. Also single gene based phylogenetic inference and alternative global markers including elongation and initiation factors, RNA polymerase subunits, DNA gyrases, heat shock and RecA proteins are of immense importance. The analysis of the sequence data involves four general steps including: (i) selection of a suitable molecule or molecules, (ii) acquisition of molecular sequences, (iii) multiple sequence alignment and (iv) phylogenetic evaluation. This chapter explains in detail how raw data of molecular sequences from any microbe may be used for the detection and identification of microorganisms using computer based bioinformatics tools.