Description

This track displays blastz alignments of the Feb. 2003/Mm3 mouse assembly to the rat genome.

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

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.

Using the Filter

The track filter can be used to turn on the chromosome color track or to filter the display output by chromosome.

When you have finished configuring the filter, click the Submit button.

Credits

The alignments are produced at UCSC, using the Blastz program provided by the Penn State Bioinformatics Group. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.