%0 Journal Article %1 Blanchette:2004ab %A Blanchette, Mathieu %A Kent, W James %A Riemer, Cathy %A Elnitski, Laura %A Smit, Arian F A %A Roskin, Krishna M %A Baertsch, Robert %A Rosenbloom, Kate %A Clawson, Hiram %A Green, Eric D %A Haussler, David %A Miller, Webb %D 2004 %J Genome Res %K Alignment, Animals, Base Biology, Cats, Cattle, Computational Computer Data, Dogs, Evaluation Evolution, Family, Genes, Genome, Homeobox, Human Humans, Mice, Molecular Molecular, Multigene Proteins, Rats, Ribosomal Sequence Sequence, Simulation, Software, Studies, fos, %N 4 %P 708--15 %R 10.1101/gr.1933104 %T Aligning multiple genomic sequences with the threaded blockset aligner %V 14 %X 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{Blanchette:2004ab, 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.}, added-at = {2007-09-17T20:19:41.000+0200}, affiliation = {Howard Hughes Medical Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA.}, 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}, biburl = {https://www.bibsonomy.org/bibtex/2603999da4e6e7a8a1aec213f1430fb55/dzerbino}, doi = {10.1101/gr.1933104}, interhash = {b09e6e292a15e550cd1d772e969cdbd9}, intrahash = {603999da4e6e7a8a1aec213f1430fb55}, issue = {4}, journal = {Genome Res}, keywords = {Alignment, Animals, Base Biology, Cats, Cattle, Computational Computer Data, Dogs, Evaluation Evolution, Family, Genes, Genome, Homeobox, Human Humans, Mice, Molecular Molecular, Multigene Proteins, Rats, Ribosomal Sequence Sequence, Simulation, Software, Studies, fos,}, language = {English}, local-url = {file://localhost/Users/danielzerbino/Documents/Papers/2004/Blanchette/Genome%20Res%202004%20Blanchette-1.pdf}, month = Apr, number = 4, pages = {708--15}, pii = {14/4/708}, pmid = {15060014}, timestamp = {2007-09-17T20:19:43.000+0200}, title = {Aligning multiple genomic sequences with the threaded blockset aligner}, uri = {papers://055852FE-1648-42FE-91D0-8CA474D2B905/Paper/p1}, volume = 14, year = 2004 }