Description

This track displays blastz alignments of the Nov. 2002 rat assembly to the mouse genome filtered to display only the best alignment for any given region of the mouse 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 radio button next to "Color track based on chromosome".

Methods

For blastz, we use 12 of 19 seeds and then score 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

We then do a second pass 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.

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 mouse genome assembly from which the alignment originated.
• Chromosome filter: To display only alignments from a specific chromosome in the mouse assembly, enter the chromosome number (in the form chrN) in the text box to the right of "Filter by chromosome". For example, to display mouse alignments from mouse chromosome 6, type "chr6". When you have finished configuring the filter, click the Submit button.

  Credits

  These alignments are contributed by Scott Schwartz of the Penn State Bioinformatics Group. The best in genome filtering is done by UCSC's axtBest program. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.