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 in the Chimp Chain track description. The chains were then processed with the programs chainNet and netChainSubset to create a reciprocal best alignment net, as described in the Chimp Net track description. Finally, single-coverage alignments were extracted from the chimp alignment net using the netToAxt program.

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 Eli & Edythe L. Broad Institute at MIT/Harvard, and Washington University School of Medicine for providing this sequence.

References

Human-Mouse Alignments with BLASTZ. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler H, and Miller W. Genome Research 2003 Jan;13(1):103-7.

Scoring pairwise genomic sequence alignments. Chiaromonte F, Yap VB, Miller W. Pac Symp Biocomput 2002;:115-26.