title: Comparison of genomic DNA sequences: solved and unsolved problems.
abstract: BACKGROUND
  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.
authors.affiliation: Department of Computer Science and Engineering, Penn State, University Park, PA 16802, USA. webb@cse.psu.edu
authors.forename: W
authors.initials: W
authors.lastname: Miller
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D016415:Sequence Alignment / Q000706:statistics & numerical data* / Q000639:trends; D012984:Software