TY  - JOUR
A1  - Blanchette, Mathieu
A1  - Kent, W. James
A1  - Riemer, Cathy
A1  - Elnitski, Laura
A1  - Smit, Arian F.A.
A1  - Roskin, Krishna M.
A1  - Baertsch, Robert
A1  - Rosenbloom, Kate
A1  - Clawson, Hiram
A1  - Green, Eric D.
A1  - Haussler, David
A1  - Miller, Webb
T1  - Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
Y1  - 2004/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 708 
EP  - 715 
DO  - 10.1101/gr.1933104 
VL  - 14 
IS  - 4 
UR  - http://genome.cshlp.org/content/14/4/708.abstract 
N2  - 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. 
ER  -