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.