Schema for chainDm3
  Database: dm6    Primary Table: chainDm3    Row Count: 1,038,532   Data last updated: 2022-10-21
fieldexampleSQL type
bin 1smallint(5) unsigned
score 2179189922double
tName chr2Lvarchar(255)
tSize 23513712int(10) unsigned
tStart 0int(10) unsigned
tEnd 23105354int(10) unsigned
qName chr2Lvarchar(255)
qSize 23011544int(10) unsigned
qStrand +char(1)
qStart 0int(10) unsigned
qEnd 22998087int(10) unsigned
id 3int(10) unsigned

Connected Tables and Joining Fields
        dm6.chainDm3Link.chainId (via chainDm3.id)
      dm6.netDm3.chainId (via chainDm3.id)

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
12179189922chr2L23513712023105354chr2L23011544+0229980873
58541478chr2L2351371252166021chrU10049037-27585092759304426488
58543405chr2L2351371252166009chrUextra29004656+16651061665845405366
58538540chr2L2351371252166021chrU10049037-35680673568875460640
58534745chr2L2351371252165885chrUextra29004656+11449121145556508950
58541736chr2L2351371252166021chrUextra29004656-2778480027785606423760
58535521chr2L2351371252165847chrUextra29004656+1234195812342557498379
58541255chr2L2351371252326014chrUextra29004656+57236335724400428982
58539567chr2L2351371252325926chrUextra29004656-1130109111301760448798
58536756chr2L2351371252325886chrUextra29004656+95981199598753482463

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

(dm3) D. mel. Chain (chainDm3) Track Description
 

Description

This track shows D. melanogaster/D. melanogaster genomic alignments using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both D. melanogaster and D. melanogaster simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The D. melanogaster sequence is from the Apr. 2006 (BDGP R5/dm3) (dm3) assembly.

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 D. melanogaster assembly or an insertion in the D. melanogaster 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 D. melanogaster 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 "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 D. melanogaster/D. melanogaster split were removed, and the resulting abbreviated genomes were aligned with blastz. The transposons were then put back into the alignments. The resulting alignments were converted into axt format and the resulting axts fed into axtChain. AxtChain organizes all the alignments between a single D. melanogaster and a single D. melanogaster chromosome into a group and makes a kd-tree out of all the gapless subsections (blocks) of the alignments. Next, maximally scoring chains of these blocks were found by running a dynamic program over the kd-tree. Chains scoring below a threshold were discarded; the remaining chains are displayed here.

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 program RepeatMasker.

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, V.B., Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-Mouse Alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).