Schema for (dm3) D. mel. Net - D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Alignment Net
  Database: dm6    Primary Table: netDm3    Row Count: 11,538
fieldexampleSQL type info
bin 1smallint(5) unsigned range
level 1int(10) unsigned range
tName chr2Lvarchar(255) values
tStart 0int(10) unsigned range
tEnd 23105354int(10) unsigned range
strand +char(1) values
qName chr2Lvarchar(255) values
qStart 0int(10) unsigned range
qEnd 22998087int(10) unsigned range
chainId 3int(10) unsigned range
ali 22997865int(10) unsigned range
score 2179189922double range
qOver -1int(11) range
qFar -1int(11) range
qDup 193097int(11) range
type topvarchar(255) values
tN 200int(11) range
qN 200int(11) range
tR 1913770int(11) range
qR 1953225int(11) range
tNewR -1int(11) range
qNewR -1int(11) range
tOldR -1int(11) range
qOldR -1int(11) range
tTrf 306674int(11) range
qTrf 216596int(11) range

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

Sample Rows

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

(dm3) D. mel. Net (netDm3) Track Description


This track shows the best D. melanogaster/D. melanogaster chain for every part of the D. melanogaster 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.


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.


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.


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).