DNA Sequencing Analysis Software for Sanger Data- Sets: Comparisons of Basic features Useful for Mutational Studies

Mutation analysis is based on the alignment and comparison of the fluorescent traces produced by Sanger DNA sequencing. Various secondary analysis sequencing software tools are available for scientific research, but as the commercial applications of genetic analysis began to grow, sequencing analysis software tools have expanded their features and uses. This paper explores software programs such as CodonCode Aligner, Geneious and Sequencher which includes sequence assembly, contig editing, and mutation detection and labeling. In an attempt to assess their features for the benefit of users we have evaluated the features based on some specific criteria. The features compared include chromatogram editing, database creation and management, quality assessment, SNP statistics, and other features useful for simple sequence analysis. These features are discussed with respect to the three platforms to gain insight into the specific areas for which they are most useful. Our comparative analysis of three software programs revealed that all the basic features required for muatiaonal analysis are similar to a few unique features in each programme. Hence end user needs to select the appropriate program.