Bioinformatics tools in marine DNA barcoding

Information science has been applied to manage the information generated in molecular biology to produce the field called Bioinformatics. Application of bioinformatics in several ways is an integral part of DNA barcode research. Since the origin of the DNA barcode concept, three major criteria were set up to test the efficiency of barcode regions. These are (i) Universal Primers to amplify the barcode region (ii) Calculation of Barcode gap (intra and interspecies distance) (iii) Species resolution power. For evaluation of these criteria, DNA barcode community is applying bioinformatics tools and algorithms in primer design, distance calculation, phylogenetic analysis, etc. DNA Barcoding produces a huge amount of Cytochrome c oxidase subunit I (COI) sequences information for species identification from animal kingdom of marine biodiversity. Similarly, Consortium of Barcode of Life (CBOL) plant group proposed plastid genes rbcL and matK either singly or in combination as the standard DNA barcode for plants (CBOL Plant Working Group 2009). ITS of the nuclear ribosomal RNA standardized as the universal barcode marker for fungi. Bioinformatics play a major role in storing of DNA barcode information, and it is easy to retrieve from the database. Software-based sequence quality assurance is main starting and check point for the production of barcode sequences. In this chapter, we discussed different tools and methods of bioinformatics and their proper utilization.