## Description

This track displays blastz alignments of the Feb. 2002 mouse draft assembly to the human genome.

## Methods

Blastz uses 12 of 19 seeds and this 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
A second pass is done 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.

## Using the Filter

The track filter can be used to turn on the chromosome color track or to filter the display output by chromosome.

- Color track To display the chromosome color track, click the on button next to "Color track based on chromosome". When the color track is activated, each of the items within the annotation track will be colored to show the chromosome in the genome assembly from which the alignment originated.
- Chromosome filter: To display only alignments from a specific chromomsome in the aligning assembly, enter the chromosome number (in the form chrN) in the text box to the right of "Filter by chromosome". For example, to display alignments from chromosome 6, type "chr6".

When you have finished configuring the filter, click the Submit button.

## Credits

The alignments are contributed by Scott Schwartz from the Penn State Bioinformatics Group. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.