Description

This track displays multiz multiple alignments of seven species of the genus Saccharomyces. The graphic display shows the alignment projected onto S. cerevisiae. Click on the alignment to see the full alignment including sequence not in S. cerevisiae.

The genomes were downloaded from:

Methods

Multiz is a multiple alignment program that takes blastz "best-in-genome" alignments (axtBest) as input. Multiz and blastz were run with the scoring matrix:
        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 over all pairs.

Credits

The multiz program was created by Webb Miller of the Penn State Bioinformatics Group. Jim Kent at UCSC wrote axtBest and the scripts to run multiz genome-wide and to display the alignments in this browser. Sequence data were provided by Washington University and the Eli & Edythe L. Broad Institute at MIT/Harvard.

References

Aligning Multiple Genomic Sequences with the Threaded Blockset Aligner. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Submitted for publication.

Human-Mouse Alignments with BLASTZ. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler H, 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.