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  Schema for Human Chain - Human (Mar. 2006/hg18) Chained Alignments
  Database: bosTau4    Primary Table: chainHg18    Row Count: 7,818,994
Format description: Summary info about a chain of alignments
fieldexampleSQL type description
bin 585smallint unsigned Indexing field to speed chromosome range queries.
score 57561double score of chain
tName chr1varchar(255) Target sequence name
tSize 161106243int unsigned Target sequence size
tStart 1744int unsigned Alignment start position in target
tEnd 3258int unsigned Alignment end position in target
qName chr13varchar(255) Query sequence name
qSize 114142980int unsigned Query sequence size
qStrand +char(1) Query strand
qStart 58653115int unsigned Alignment start position in query
qEnd 58654660int unsigned Alignment end position in query
id 71673int unsigned chain id

  Connected Tables and Joining Fields
        bosTau4.chainHg18Link.chainId (via chainHg18.id)
      bosTau4.netHg18.chainId (via chainHg18.id)

  Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
58557561chr116110624317443258chr13114142980+586531155865466071673
585314151chr1161106243377114370chr13114142980+58644820586585626345
5856787chr116110624344484606chr7158821424-26753087267532445004207
5859142chr11611062431730417666chr11134452384+55356168553565423918981
58538230chr11611062432370728186chr11134452384+5529454855298393219191
585225103chr11611062432410942342chr11134452384+55325819553447749293
585695788chr11611062432527889607chr11134452384+55341254554402812674
58569157chr11611062432612528350chr11134452384+553616165536389349602
58511601chr11611062432713428065chr12132349534-78291602782925173011473
5859666chr11611062432714027607chr4191273063-1498526461498530903715129

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


  Human Chain (chainHg18) Track Description
 

Description

This track shows alignments of human (hg18, Mar. 2006) 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 human 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 human 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.

Methods

Transposons that have been inserted since the human/cow split were removed from the assemblies. The abbreviated genomes were aligned with blastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human 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:

ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

Chains scoring below a threshold were discarded; the remaining chains are displayed in this track.

Credits

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.

References

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.