## Description

This track displays multiz alignments of the human Apr. 2003 (hg15) assembly and the mouse Feb. 2003 (mm3) draft assembly to the $organism genome.

## Methods

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.

## Credits

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.

## References

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.