TY  - JOUR
A1  - Brudno, Michael
A1  - Do, Chuong B.
A1  - Cooper, Gregory M.
A1  - Kim, Michael F.
A1  - Davydov, Eugene
A1  - Program, NISC Comparative Sequencing
A1  - Green, Eric D.
A1  - Sidow, Arend
A1  - Batzoglou, Serafim
T1  - LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
Y1  - 2003/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 721 
EP  - 731 
DO  - 10.1101/gr.926603 
VL  - 13 
IS  - 4 
UR  - http://genome.cshlp.org/content/13/4/721.abstract 
N2  - To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. We present LAGAN, a system for rapid global alignment of two homologous genomic sequences, and Multi-LAGAN, a system for multiple global alignment of genomic sequences. We tested our systems on a data set consisting of greater than 12 Mb of high-quality sequence from 12 vertebrate species. All the sequence was derived from the genomic region orthologous to an ∼1.5-Mb region on human chromosome 7q31.3. We found that both LAGAN and Multi-LAGAN compare favorably with other leading alignment methods in correctly aligning protein-coding exons, especially between distant homologs such as human and chicken, or human and fugu. Multi-LAGAN produced the most accurate alignments, while requiring just 75 minutes on a personal computer to obtain the multiple alignment of all 12 sequences. Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance. Our systems are publicly available at http://lagan.stanford.edu. 
ER  -