Description

This track displays Blastz alignments of the Nov. 2002 rat draft assembly to the human genome filtered to display only the best alignment for any given region of the human genome. The track has an optional feature that color codes alignments to indicate the rat chromosomes from which they are derived. 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 now do a second pass at reduced stringency (7mer seeds and MSP threshold of K=2200) to attempt to fill in gaps (up to about 10Kbp). 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.