RT Journal
A1 Brudno, Michael
A1 Poliakov, Alexander
A1 Salamov, Asaf
A1 Cooper, Gregory M.
A1 Sidow, Arend
A1 Rubin, Edward M.
A1 Solovyev, Victor
A1 Batzoglou, Serafim
A1 Dubchak, Inna
T1 Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
JF Genome Research 
JO Genome Research 
YR 2004 
FD April 01 
VO 14 
IS 4 
SP 685 
OP 692 
DO 10.1101/gr.2067704 
UL http://genome.cshlp.org/content/14/4/685.abstract 
AB 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.