Aligning multiple genomic sequences with the threaded blockset aligner. Blanchette, M., Kent, W J., Riemer, C., Elnitski, L., Smit, A. F A., Roskin, K. M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E. D., Haussler, D., & Miller, W. Genome Res, 14(4):708–715, 2004.
doi  abstract   bibtex   
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 output of TBA can be projected onto any genome chosen as a reference, thus guaranteeing that different projections present consistent predictions of which genomic positions are orthologous. This capability is illustrated using a new visualization tool to view TBA-generated alignments of vertebrate Hox clusters from both the mammalian and fish perspectives. Experimental evaluation of alignment quality, using a program that simulates evolutionary change in genomic sequences, indicates that TBA is more accurate than earlier programs. To perform the dynamic-programming alignment step, TBA runs a stand-alone program called MULTIZ, which can be used to align highly rearranged or incompletely sequenced genomes. We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.
@Article{blanchette04aligning,
  author    = {Blanchette, Mathieu and Kent, W James and Riemer, Cathy and Elnitski, Laura and Smit, Arian F A. and Roskin, Krishna M. and Baertsch, Robert and Rosenbloom, Kate and Clawson, Hiram and Green, Eric D. and Haussler, David and Miller, Webb},
  title     = {Aligning multiple genomic sequences with the threaded blockset aligner.},
  journal   = {Genome Res},
  year      = {2004},
  volume    = {14},
  number    = {4},
  pages     = {708--715},
  abstract  = {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 output of TBA can be projected onto any genome chosen as a reference, thus guaranteeing that different projections present consistent predictions of which genomic positions are orthologous. This capability is illustrated using a new visualization tool to view TBA-generated alignments of vertebrate Hox clusters from both the mammalian and fish perspectives. Experimental evaluation of alignment quality, using a program that simulates evolutionary change in genomic sequences, indicates that TBA is more accurate than earlier programs. To perform the dynamic-programming alignment step, TBA runs a stand-alone program called MULTIZ, which can be used to align highly rearranged or incompletely sequenced genomes. We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.},
  doi       = {10.1101/gr.1933104},
  keywords  = {Animals; Base Sequence; Cats; Cattle; Dogs; Evaluation Studies as Topic; Genes, Homeobox; Genes, fos; Humans; Mice; Molecular Sequence Data; Multigene Family; Rats; Ribosomal Proteins; Sequence Alignment;},
  optmonth  = apr,
  owner     = {fhufsky},
  pmid      = {15060014},
  timestamp = {2014.01.13},
}

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