## Description

This track displays multiz alignments of the mouse Feb. 2003 (mm3) draft assembly and the rat Jun. 2003 (rn3) assembly to the human genome.

## Methods

Multiz is a multiple alignment program that takes blastz "Best-in-Genome" alignments (axtBest or axtNet) as input. For human/rodent alignments, 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

For the mouse/rat alignments the following matrix was used:

            A     C     G     T
      A    86  -135   -68  -157
      C  -135   100  -148   -68
      G   -68  -148   100  -135
      T  -157   -68  -135    86

      O = 600, E = 50

The overall score is the sum of the score over all pairs.

## Credits

This track was created at UCSC using a program called humor (HUman-MOuse-Rat), which is a special variant of the Multiz program created by Minmei Hou and Webb Miller of 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

Blanchette, M, Kent, WJ, Riemer, C, Elnitski, L, Smit, AF, Roskin, KM, Baertsch, R, Rosenbloom, K, Clawson, H, Green, ED, Haussler, D, Miller, W (2004). Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14(4):708-15.

Chiaromonte F, Yap VB, Miller W (2002). Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002;:115-26.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and Miller W (2003). Human-Mouse Alignments with BLASTZ. Genome Res. 13(1):103-7.