## Description

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 has an optional feature that color codes alignments to indicate the mouse chromosomes from which they are derived. To activate the color feature, click the on radio button next to "Color track based on chromosome".

## Methods

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.

## Credits

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. The web display is by Jim Kent.