This track shows alignments of the human genome with itself, using
a gap scoring system that allows longer gaps than traditional
affine gap scoring systems. The system can also tolerate gaps
in both sets of sequence simultaneously. After filtering out the
"trivial" alignments produced when identical locations of the
genome map to one another (e.g. chrN mapping to chrN),
the remaining alignments point out areas of duplication within the
human genome. The pseudoautosomal regions of chrX and chrY are an
exception: in this assembly, these regions have been copied from chrX into
chrY, resulting in a large amount of self chains aligning in these positions
on both chromosomes.
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 query assembly or an
insertion in the target assembly. Double lines represent more complex gaps
that involve substantial sequence in both the query and target assemblies.
This may result from inversions, overlapping deletions, an abundance of local
mutation, or an unsequenced gap in one of the assemblies. In cases where
multiple chains align over a particular region of the human genome, the
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
In the "pack" and "full" display
modes, the individual feature names indicate the chromosome, strand, and
location (in thousands) of the match for each matching alignment.
Display Conventions and Configuration
By default, the chains to chromosome-based assemblies are colored
based on which chromosome they map to in the aligning organism. To turn
off the coloring, check the "off" button next to: Color
track based on chromosome.
To display only the chains of one chromosome in the aligning
organism, enter the name of that chromosome (e.g. chr4) in box next to:
Filter by chromosome.
The genome was aligned to itself using blastz. Trivial alignments were
filtered out, and the remaining alignments were converted into axt format
using the lavToAxt program. The axt alignments were fed into axtChain, which
organizes all alignments between a single target chromosome and a single
query chromosome into a group and creates a kd-tree out of the gapless
subsections (blocks) of the alignments. A dynamic program was then run over
the kd-trees to find the maximally scoring chains of these blocks.
The following matrix was used:
Chains scoring below a minimum score of 2,000 were discarded;
the remaining chains are displayed in this track.
Blastz was developed at Pennsylvania State University by
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from
Lineage-specific repeats were identified by Arian Smit and his
The axtChain program was developed at the University of California
at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
The browser display and database storage of the chains were generated
by Robert Baertsch and Jim Kent.
Chiaromonte F, Yap VB, Miller W.
Scoring pairwise genomic sequence alignments.
Pac Symp Biocomput 2002, 115-26 (2002).
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W.
Human-mouse alignments with BLASTZ.
Genome Res. 2003 Jan;13(1):103-7.