This track displays "reciprocal best" human/chimpanzee genomic alignment chains. These alignments were generated using blastz and blat alignments of chimpanzee genomic sequence from the Nov. 2003 (panTro1) 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 $organism simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.
The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the genome of the non-$organism species or an insertion in the $organism assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or 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 chromosome, strand, and location (in thousands) of the match for each matching alignment.
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 chromosome and a single $organism chromosome into a group and creates a kd-tree from all the gapless subsections (blocks) of the alignments. Next, 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 sequences 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 "all chains"
Due to the draft nature of this initial genome assembly, this chain track and the companion net track were generated using a "reciprocal best" strategy. This strategy attempts to minimize paralog fill-in for missing orthologous chimp sequence by filtering out of the human net all sequences not in the chimp side of the net.
First, the merged blastz and blat chains were used to generate an alignment net, using the program chainNet (described on the Chimp Recip Net track description page). Next, the subset of chains in the chimp-reference net were extracted and used for an additional netting step. The resulting human-reference net was used to generate the reciprocal best Chimp Recip Net browser track. Non-syntenic sequences smaller than 50 bases were filtered out. Finally, chains extracted from this net are displayed on the Chimp Recip Chain browser track.
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 by Jim Kent at UCSC.
Chiaromonte F, Yap VB, Miller W (2002). Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002;:115-26.
Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D (2003). Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489 Sep 30 2003.
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and Miller W (2003). Human-Mouse Alignments with BLASTZ. Genome Res. 13(1):103-7.