## Description

This track displays blastz alignments of the $o_organism assembly ($o_db, $o_date) to the $organism genome, filtered by axtBest and subsetAxt with very stringent constraints as described below. The track has an optional feature that color codes alignments to indicate the chromosomes from which they are derived in the aligning assembly. To activate the color feature, click the on button next to "Color track based on chromosome" on the track description page.

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

## Methods

For blastz, 12 of 19 seeds were used and then scored 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

A second pass was made 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 were abridged during this alignment.

AxtBest was used to select only the best alignment for any given region of the genome. SubsetAxt was 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

This track has a filter that can be used to change the display mode, turn on the chromosome color track, or filter the display output by chromosome. The filter is located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu.

- 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 aligning genome assembly from which the alignment originated.
- Chromosome filter: To display only alignments from a specific chromomsome in the aligning assembly, type 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 were provided by the Mouse Genome Sequencing Consortium.

## References

Chiaromonte, F., Yap, V.B., Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103-107 (2003).