Comparison of genomic DNA sequences: solved and unsolved problems

MOTIVATION The DNA sequences of entire genomes are being determined at a rapid rate. Whereas initial genome sequencing efforts were for organisms chosen to be widely spaced in the tree of life, there is a growing emphasis on projects to sequence a species that is sufficiently similar to an already-sequenced species to allow direct comparison of those two DNA sequences. This and other changes in genome sequencing strategies have created a strong need for new methods to compare genomic sequences. RESULTS We sketch the current state of software for comparing genomic DNA sequences and outline research directions that we believe are likely to result in important advances in practice.