Comparison of genomic sequences using the Hamming distance

Abstract

The paper considers the problem of homogeneity among groups by comparison of genomic sequences. Some alternative procedures that attach less emphasis on the likelihood approach, and more on alternative measures that deal with similar homogeneity problems are considered here. On this approach, a one-sided hypothesis test is considered and the classical ANOVA decomposition can be directly adapted to sample measures based on the Hamming distance, without necessarily going through their second moments. Some results of U-statistics theory will be useful for the decomposition of the test statistic and to find its asymptotic distribution. An application of this test with real data is shown and the p-value of the test statistic is found via bootstrap resampling.