Description
This track displays blastz alignments of the Feb. 2002 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 selects only the best alignment for any given region
of the genome.
SubsetAxt was 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.