This track displays blastz alignments of the Feb. 2003 mouse draft assembly to the human genome filtered to display only the best alignment for any given region of the human genome. The track shows a graph of the score of the alignment.
For blastz, we use 12 of 19 seeds and then score using:
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
We then do a second pass at reduced stringency (7mer seeds and MSP threshold of K=2200) to attempt to fill in gaps of up to about 10K bp. Lineage specific repeats are abridged during this alignment.
The track filter can be used to turn on the chromosome color track or to filter the display output by chromosome.
When you have finished configuring the filter, click the Submit button.
These alignments are contributed by Scott Schwartz from the Penn State Bioinformatics Group. The best in genome filtering is done by UCSC's axtBest program. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.
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.