Biology Reference
In-Depth Information
Figure 11:
Three domain classifi cation of living world based on 16S rRNA sequencing.
The 16S rRNA gene sequences are easy to align that allow comparison between strains. This is a
crucial step in phylogenetic analysis (Swofford
et al
., 1996). In alignment, the sequences are arranged
in such a manner by inserting gaps so that the homologous positions of sequences are placed in the
same columns of the data matrix. A number of computer programmes have been used for aligning
the sequences, e.g. GenBank or EBI (European Bioinformatics Institute), Ribosomal Data Base
Project (RDP) and Antwerpen Projects. Further, a variety of individual software tools for sequence
editing, alignment and phylogenetic analyses are available from different software packages such
as phylogeny inference package (PHYLIP; Felsenstein, 1989), Maximum likelihood (ML method;
FastDNAml; Olsen
et al
., 1994); molecular phylogenetics based on Maximum-likelihood (Molphy-
Version 2.3), multiple sequence alignment (ClustalW; Thompson
et al
., 1994; Chenna
et al
., 2003)
and ARB software (Ludwig
et al
., 2004; accessible at http://www.arb-home.de). Although ARB
software initially was designed for rRNA data, it can now be used for any nucleic acid or amino acid
sequence as well. This software is helpful in aligning the sequences through primary structure data
that contains processed aligned sequences for comparison. It can be linked via local or worldwide
networks. Tools for data import and export, primary and secondary structure editing, specifi c
hybridization probe design are the additional features of the ARB software. ClustalW and ClustalX
version 2.0 multiple sequence alignment programmes have been completely rewritten in C++ and
made available at http://www.ebi.ac.uk/tools/clustalw2 by Larkin
et al
. (2007).
At this stage, it is required to know the defi nitions of gene terminology used while drawing
molecular phylogenetic relationships: (i) homologues are those genes that have descended from
a common ancestor (e.g. all globin genes); (ii) orthologues are those homologous genes that have
diverged from each other after speciation events (e.g. human β- and chimp β-globin); (iii) paralogues
are those homologous genes that have diverged from each other after gene duplication events (e.g.
β- and gama-globin) and (iv) xenologs are those homologous genes that have diverged from each
other after LGT events (e.g. antibiotic resistance genes in bacteria). Positional homology is a specifi c
amino acid or nucleotide positions in different genes. The methods of predicting gene function when
