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Several analyses are conducted to explain the different genome-wide patterns of the mutational mechanisms that lead to the origination of new genes in Drosophila melanogaster species subgroup. The results prove that the de novo origination from noncoding sequences and the retroposition mechanism play an extremely significant role in the origin of these new genes.

The sequence divergences of several different retrotransposon sequences are measured to determine the base substitution rate and the mutation rate of the CpG dinucleotides and non-CpG DNA. The mutation rate of non-CpG DNA is shown to be completely dependent on the varying content of local CpG.

Regional analysis of nucleotide substitution rates along human genes and their flanking regions were performed to examine the effect of mutational mechanisms associated with transcription in germ line cells. Results shed light on the mutational patterns induced by cytosine deaminase in the somatic hypermutation (SHM), which targets single-stranded DNA at the 5' ends of genes.

Sequence from BAC clones spanning chicken microchromosome GGA28 is analyzed to facilitate functional and evolutionary analysis of one especially gene-rich, rearrangement-prone genomic region. Results reveal that chromosome rearrangement may not have been random over vertebrate evolution but positioned preferentially within specific fragile regions.

This article describes a DNA mutation detection method based on base-specific cleavage of polymerase chain reaction (PCR) products and their separation by matrix-assisted laser desorption ionization-mass spectrometry. The technique is validated by its ability to detect a polymorphism in the 3' untranslated region of ILI2p40 from a double-stranded PCR product and a single nucleotide polymorphism between two mouse strains.