## Description

This track displays blastz alignments of the Feb. 2003 mouse draft assembly to the human genome, filtered by axtBest and subsetAxt with very stringent constraints as described below.

Each item in the display is identified by the chromosome, strand, and location of the match (in thousands).

## 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. axtBest is used to select only the best alignment for any given region of the genome. subsetAxt is then run on axtBest-filtered alignments with this matrix:

          A     C     G     T
    A   100  -200  -100  -200
    C  -200   100  -200  -100
    G  -100  -200   100  -200
    T  -200  -100  -200   100

with a gap open penalty of 2000 and a gap extension penalty of 50. The minimum score threshold was 3400.

## 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. The best in genome filtering is done by UCSC's axtBest and subsetAxt programs. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.