Description

This track displays blastz alignments of the Feb. 2002 mouse draft assembly to the human genome filtered so that only the best alignment for any given region of the human genome is displayed.

Methods

For blastz use 12 of 19 seeds and then score using
 ACGT
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 However, we now do a second pass at reduced stringency (7mer seeds and MSP threshold of K=2200) to attempt to fill in gaps (up to about 10Kbp). Also, lineage specific repeats are abridged during this alignment.

Credits

Alignments contributed by Scott Schwartz, Penn State Bioinformatics Group. Best in genome filtering by UCSC's axtBest program.