## Description

This track displays blastz and untranslated blat alignments of the 13 Nov. 2003 chimpanzee draft assembly to the human genome. The alignments are filtered to display only the best alignment for any given region of the human genome. The track shows a graph of the score of the alignment.

## Methods

The alignments were generated by blastz on repeatmasked sequence using the following human/chimp scoring matrix:

         A    C    G    T
    A   100 -300 -150 -300
    C  -300  100 -300 -150
    G  -150 -300  100 -300
    T  -300 -150 -300  100

    K = 4500, L = 3000,  Y=3400, H=2000

Following blastz, a DNA blat of unmasked sequence was done to place additional scaffolds. Both alignments were processed by the axtChain program, and both chains were merged to create a set of "all chains", as described on the Chimp Chain track description page The chains were then processed with the programs chainNet and netChainSubset to create a reciprocal best alignment net, as described on the Chimp Net track description page. Finally, single-coverage alignments were extracted from the chimp alignment net using the netToAxt program.

## Using the Filter

This track has a filter that can be used to change the display mode, turn on the chromosome color track, or filter the display output by chromosome. The filter is located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu.

- 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 aligning genome assembly from which the alignment originated.
- Chromosome filter: To display only alignments from a specific chromomsome in the aligning assembly, type 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

The chimp sequence used in this track was obtained from the 13 Nov. 2003 Arachne assembly. We'd like to thank the National Human Genome Research Institute (NHGRI), the Broad Institute, and Washington University St. Louis School of Medicine for providing this sequence.

## References

Chiaromonte, F., Yap, V.B., Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103-107 (2003).