Description
This track displays blastz alignments of the Nov. 2002 Rat
assembly to the mouse genome.
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 (up to about 10K bp).
Lineage specific repeats are abridged during this alignment.
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
chromosome 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,
Penn State Bioinformatics Group. Mouse sequence data are provided by the
Mouse Genome Sequencing Consortium.