@article{Brudno01042004,
author = {Brudno, Michael and Poliakov, Alexander and Salamov, Asaf and Cooper, Gregory M. and Sidow, Arend and Rubin, Edward M. and Solovyev, Victor and Batzoglou, Serafim and Dubchak, Inna}, 
title = {Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human},
volume = {14}, 
number = {4}, 
pages = {685-692}, 
year = {2004}, 
doi = {10.1101/gr.2067704}, 
abstract ={We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment and consists of two main steps: (1) alignment of the mouse and rat genomes, and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human, and 97% of all alignments with human sequence >100 kb agree with a three-way synteny map built independently, using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment, and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.}, 
URL = {http://genome.cshlp.org/content/14/4/685.abstract}, 
eprint = {http://genome.cshlp.org/content/14/4/685.full.pdf+html}, 
journal = {Genome Research} 
}