Description

This track displays human/chimpanzee genomic alignment chains. These alignments were generated using blastz and blat alignments of chimpanzee genomic sequence from the 13 Nov. 2003 Arachne chimpanzee draft assembly.

Alignments were performed using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chimp and $organism simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

The graphical display shows boxes joined together by single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are often due to gaps caused by unsequenced portions of the chimp genome, but occasionally represent deletion in the chimp or insertion in the human relative to the chimp. Double lines represent gaps in the chain where sequence is present in both species but they do not align, or cases where there is an unsequenced gap in one species. In cases where there are multiple chains over a particular portion of the $organism genome, chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the fuller display modes, the individual feature names indicate the scaffold name, strand, and location (in thousands) of the match for each matching alignment.

Methods

The alignments were generated by blastz on repeatmasked sequence using the following chimp/human 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
The resulting alignments were processed by the axtChain program. AxtChain organizes all the alignments between a single chimp scaffold and a single $organism chromosome into a group and makes a kd-tree out of all the gapless subsections (blocks) of the alignments. The maximally-scoring chains of these blocks were found by running a dynamic program over the kd-tree. Chains scoring below a certain threshold were discarded.

To place additional chimp scaffolds that weren't initially aligned by blastz, a DNA blat of the unmasked sequence was performed. The resulting blat alignments were also chained, and then merged with the blastz-based chains produced in the previous step to produce the chains displayed in this track.

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.

Blastz was developed at Pennsylvania State University by Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

The chaining and netting programs were developed at the University of California at Santa Cruz by Jim Kent.

The browser display and database storage of the chains were made by Robert Baertsch and Jim Kent.

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.