This track displays blastz alignments of the $o_organism assembly ($o_db, $o_date) to the $organism genome, filtered to display only the best alignment for any given region of the $organism genome.
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:
When you have finished configuring the filter, click the Submit button to return to the annotation tracks 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.
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. 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).