DNA Sequence Analysis

Abstract

Abstract Recent advances in deoxyribonucleic acid (DNA) sequencing technology have produced a massive amount of nucleotide sequences, which are stored in DNA databanks and genomic data repositories. Furthermore, comprehensive analyses of transcriptional and genomic elements have uncovered an elaborate system of gene expression that broadens our understanding of fundamental biological phenomena. The analysis of DNA data has therefore become essential to predict gene function or detect regulatory motifs through comparative studies. In this article, DNA databases, homology search tools and sequence alignment methods are surveyed. The concept of distance between genes and how to calculate this measure using DNA or amino acid sequences and introducing several commonly used techniques for phylogenetic analysis and tree evaluation are also described. Key concepts Advances in DNA sequencing technology have produced an unprecedented amount of sequence data. The DNA Data Bank of Japan (DDBJ), the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI) are the three major sequence data repositories. They exchange data periodically, and maintain various services for data search and retrieval. Similarity searching, alignment of sequences, prediction of function and reconstruction of the evolutionary history (phylogenetic tree) of a group of species are among the most commonly used techniques for sequence analysis. BLAST (similarity searching), ClustalW (sequence alignment), Pfam (protein domains) and TRANSFAC (transcription factors) are popular tools and resources. The genetic distance, a measure of evolutionary similarity, is usually calculated as the number of nucleotide or amino acid differences (substitutions) among sequences. Nucleotide substitutions are synonymous (not affecting the codified amino acid) or nonsynonymous (triggering an amino acid change). Distance‐ and character‐based methods can be used to reconstruct phylogenetic trees. Distance‐based methods reconstruct the tree from an estimation of the evolutionary distance among taxa. Character‐based methods derive the phylogeny directly from the observable state of characters in the taxa. The bootstrap method is commonly used to determine the quality of an inferred phylogeny.