This track shows blastz alignments of the $o_organism assembly ($o_db, $o_date) to the $organism genome. 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.
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.
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.
When you have finished configuring the filter, click the Submit button.
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.
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).