This track displays multiz alignments of the Feb. 2003 mouse draft assembly and the rat Jan. 2003 assembly to the $organism genome.
Multiz is a multiple alignment program that takes blastz /axtBest alignments as input. It uses the same scoring matrix as blastz between pairs of sequences:
A C G T
A 91 -114 -31 -123
C -114 100 -125 -31
G -31 -125 100 -114
T -123 -31 -114 91
O = 400, E = 30, K = 3000, L = 3000, M = 50
The overall score is the sum of the score between all pairs.
Multiz was created by Minmei Hou and Webb Miller from the Penn State Bioinformatics Group. Jim Kent wrote axtBest and the scripts to run multiz genome-wide and to display the alignments in this browser. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium. Rat sequence data are provided by the Rat Sequencing Consortium.
Human-Mouse Alignments with BLASTZ. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and Miller W. Genome Research 2003 Jan;13(1):103-7.
Scoring pairwise genomic sequence alignments. Chiaromonte F, Yap VB, Miller W. Pac Symp Biocomput 2002;:115-26.