## Description

This track displays blastz alignments of the $o_Organism assembly ($o_db, $o_date) to the $organism genome.

## Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. Each item in the display is identified by the chromosome, strand, and location of the match (in thousands).

The track description page offers the following filter and configuration options:

- 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 to return to the annotation tracks page.

## 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.

## Credits

These alignments were contributed by Scott Schwartz of the Penn State Bioinformatics Group. The best-in-genome filtering was done using UCSC's axtBest program.

## 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).