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  Schema for Dog Chain - Dog (May 2005/canFam2) Chained Alignments
  Database: bosTau4    Primary Table: chainCanFam2    Row Count: 3,323,984
Format description: Summary info about a chain of alignments
fieldexampleSQL type description
bin 585smallint unsigned Indexing field to speed chromosome range queries.
score 13231double score of chain
tName chr1varchar(255) Target sequence name
tSize 161106243int unsigned Target sequence size
tStart 192int unsigned Alignment start position in target
tEnd 524int unsigned Alignment end position in target
qName chr22varchar(255) Query sequence name
qSize 64401119int unsigned Query sequence size
qStrand -char(1) Query strand
qStart 20715940int unsigned Alignment start position in query
qEnd 20716467int unsigned Alignment end position in query
id 1412640int unsigned chain id

  Connected Tables and Joining Fields
        bosTau4.chainCanFam2Link.chainId (via chainCanFam2.id)
      bosTau4.netCanFam2.chainId (via chainCanFam2.id)

  Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

  Dog Chain (chainCanFam2) Track Description


This track shows alignments of dog (canFam2, May 2005) to the cow genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and cow 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 dog assembly or an insertion in the cow 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 multiple chains align over a particular region of the cow 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 pseudogenes.

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.


Transposons that have been inserted since the dog/cow split were removed from the assemblies. The abbreviated genomes were aligned with blastz, and the transposons were then added back in. The resulting alignments were converted into psl format using the lavToPsl program. The psl alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single cow 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 threshold 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 Ross Hardison.

Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program.

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.

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.