Aligning multiple genomic sequences with the threaded blockset aligner.

@article{Blanchette2004AligningMG,
  title={Aligning multiple genomic sequences with the threaded blockset aligner.},
  author={Mathieu Blanchette and W. James Kent and Cathy Riemer and Laura Elnitski and Arian F. A. Smit and Krishna M. Roskin and Robert Baertsch and Kate R. Rosenbloom and Hiram Clawson and Eric D. Green and David Haussler and Webb Miller},
  journal={Genome research},
  year={2004},
  volume={14 4},
  pages={708-15}
}
We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for "threaded blockset aligner") builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are not addressed. TBA is designed to be appropriate for aligning many, but by no means all, megabase-sized regions of multiple mammalian genomes. The… CONTINUE READING
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