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  Schema for Mouse Chain - Mouse (July 2007/mm9) Chained Alignments
  Database: bosTau4    Primary Table: chainMm9    Row Count: 3,023,757
Format description: Summary info about a chain of alignments
fieldexampleSQL type description
bin 585smallint unsigned Indexing field to speed chromosome range queries.
score 18382double score of chain
tName chr1varchar(255) Target sequence name
tSize 161106243int unsigned Target sequence size
tStart 1716int unsigned Alignment start position in target
tEnd 2405int unsigned Alignment end position in target
qName chr14varchar(255) Query sequence name
qSize 125194864int unsigned Query sequence size
qStrand +char(1) Query strand
qStart 86551890int unsigned Alignment start position in query
qEnd 86552555int unsigned Alignment end position in query
id 495396int unsigned chain id

  Connected Tables and Joining Fields
        bosTau4.chainMm9Link.chainId (via chainMm9.id)
      bosTau4.netMm9.chainId (via chainMm9.id)

  Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
58518382chr116110624317162405chr14125194864+8655189086552555495396
5855985chr116110624349825354chr14125194864+86544476865448202493735
58596880chr1161106243695613368chr14125194864+86547047865552887940
5855566chr11611062432440324615chr2181748087-93870061938702612565781
5854783chr11611062432444724607chr2181748087+87862814878629742710260
585118744chr11611062432566543476chr2181748087-93931847939662575204
58552373chr11611062432656428212chr2181748087+878642628786580732717
58559931chr11611062432688028395chr2181748087-938724069387389224109
58521969chr11611062432694628190chr2181748087-9485842994859598301630
58511182chr11611062432714028181chr10129993255+1292128261292138581690619

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


  Mouse Chain (chainMm9) Track Description
 

Description

This track shows alignments of mouse (mm9, July 2007) 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 mouse 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 mouse 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 mouse/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 psl format using the lavToPsl program. The psl alignments were fed into axtChain, which organizes all alignments between a single mouse 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.