Description
This track displays blastz alignments of the Feb. 2002 mouse 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 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 genome assembly from which the alignment
originated.
- Chromosome filter: To display only alignments from a specific
chromomsome 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
These alignments are contributed by Scott Schwartz from 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.