Description

This track displays blastz alignments of the Apr. 2003 Human 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 were generated at UCSC using the blastz tool developed by the Penn State Bioinformatics Group. Rat sequence data are provided by the Rat Genome Sequencing Consortium.