Schema for D. melanogaster Net - D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Alignment Net
  Database: DmojImproved    Primary Table: netdm3    Row Count: 104,112
fieldexampleSQL type info
bin 585smallint(5) unsigned range
level 1int(10) unsigned range
tName improved_6498varchar(255) values
tStart 71382int(10) unsigned range
tEnd 72653int(10) unsigned range
strand +char(1) values
qName chr3Lvarchar(255) values
qStart 24506495int(10) unsigned range
qEnd 24507768int(10) unsigned range
chainId 2109int(10) unsigned range
ali 1258int(10) unsigned range
score 48418double range
qOver -1int(11) range
qFar -1int(11) range
qDup 0int(11) range
type topvarchar(255) values
tN 0int(11) range
qN 0int(11) range
tR 875int(11) range
qR 880int(11) range
tNewR -1int(11) range
qNewR -1int(11) range
tOldR -1int(11) range
qOldR -1int(11) range
tTrf 0int(11) range
qTrf 0int(11) range

Sample Rows
 
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851improved_64987138272653+chr3L24506495245077682109125848418-1-10top00875880-1-1-1-100
5851improved_64987320973542+chrU248861724889491145733010413-1-1332top0000-1-1-1-100
5851improved_64989794898131+chrX1431921214319395126881839418-1-10top0000-1-1-1-100
5861improved_6498143084143213+chr3RHet22830762283202167541267358-1-1125top0000-1-1-1-100
5861improved_6498213082243422+chrX1434699514348280778234015623-1-10top002469621-1-1-1-17160
5862improved_6498213222243222+chrX1434713514348080000-1-1-1gap002469621-1-1-1-17160
5871improved_6498307348307799-chr3L2435156724352024519045112691-1-1457top00269149-1-1-1-100
5871improved_6498307799307889+chrUextra307288230729726958902791-1-190top007976-1-1-1-100
5871improved_6498308172308533+chrU19039419074740323507341-1-10top0000-1-1-1-100
5872improved_6498308371308381+chrU190595190595000-1-1-1gap0000-1-1-1-100

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

D. melanogaster Net (netdm3) Track Description
 

Description

This track shows the best D. melanogaster/D. mojavensis chain for every part of the D. mojavensis genome. It is useful for finding orthologous regions and for studying genome rearrangement. The D. melanogaster sequence used in this annotation is from the Apr. 2006 (BDGP R5/dm3) (dm3) assembly.

Display Conventions and Configuration

In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth.

In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.

Individual items in the display are categorized as one of four types (other than gap):

  • Top - the best, longest match. Displayed on level 1.
  • Syn - line-ups on the same chromosome as the gap in the level above it.
  • Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation.
  • NonSyn - a match to a chromosome different from the gap in the level above.

Methods

Chains were derived from blastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Credits

The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.

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 browser display and database storage of the nets were made by Robert Baertsch and Jim Kent.

References

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).