Schema for C. briggsae Net - C. briggsae (Jan. 2007 (WUGSC 1.0/cb3)) Alignment Net
  Database: ce6    Primary Table: netCb3    Row Count: 220,335   Data last updated: 2008-06-04
Format description: Database representation of a net of alignments.
fieldexampleSQL type info description
bin 9smallint(5) unsigned range Indexing field to speed chromosome range queries.
level 1int(10) unsigned range Level of alignment
tName chrVvarchar(255) values Target chromosome
tStart 1367int(10) unsigned range Start on target
tEnd 3756858int(10) unsigned range End on target
strand +char(1) values Orientation of query. + or -
qName chrV_randomvarchar(255) values Query chromosome
qStart 460332int(10) unsigned range Start on query
qEnd 1558501int(10) unsigned range End on query
chainId 45int(10) unsigned range Associated chain Id with alignment details
ali 134069int(10) unsigned range Bases in gap-free alignments
score 3672087double range Score - a number proportional to 100x matching bases
qOver -1int(11) range Overlap with parent gap on query side. -1 for undefined
qFar -1int(11) range Distance from parent gap on query side. -1 for undefined
qDup 55025int(11) range Bases with two or more copies in query. -1 for undefined
type topvarchar(255) values Syntenic type: gap/top/syn/nonsyn/inv
tN 0int(11) range Unsequenced bases on target. -1 for undefined
qN 0int(11) range Unsequenced bases on query. -1 for undefined
tR 849216int(11) range RepeatMasker bases on target. -1 for undefined
qR 238485int(11) range RepeatMasker bases on query. -1 for undefined
tNewR -1int(11) range Lineage specific repeats on target. -1 for undefined
qNewR -1int(11) range Lineage specific repeats on query. -1 for undefined
tOldR -1int(11) range Bases of ancient repeats on target. -1 for undefined
qOldR -1int(11) range Bases of ancient repeats on query. -1 for undefined
tTrf 185307int(11) range Bases of tandem repeats on target. -1 for undefined
qTrf 21245int(11) range Bases of tandem repeats on query. -1 for undefined

Connected Tables and Joining Fields
        ce6.chainCb3.id (via netCb3.chainId)
      ce6.chainCb3Link.chainId (via netCb3.chainId)

Sample Rows
 
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
91chrV13673756858+chrV_random4603321558501451340693672087-1-155025top00849216238485-1-1-1-118530721245
5852chrV15101523+chrV_random460500460500000-1-1-1gap0000-1-1-1-100
5852chrV15341550+chrV_random460511460511000-1-1-1gap0000-1-1-1-100
5852chrV15751589+chrV_random460534460534000-1-1-1gap0000-1-1-1-100
5852chrV16071627+chrV_random460552460552000-1-1-1gap0000-1-1-1-100
5852chrV17081720+chrV_random460659460659000-1-1-1gap0030-1-1-1-100
5852chrV17381759+chrV_random460677460677000-1-1-1gap0030-1-1-1-100
5852chrV18372831+chrV_random460752462283000-1-1-1gap00694941-1-1-1-1950
5852chrV30255530+chrV_random462482462679000-1-1-1gap00693139-1-1-1-100
5852chrV55615578+chrV_random462710462718000-1-1-1gap0000-1-1-1-100

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

C. briggsae Net (netCb3) Track Description
 

Description

This track shows the best C. briggsae/C. elegans chain for every part of the C. elegans genome. It is useful for finding orthologous regions and for studying genome rearrangement. The C. briggsae sequence used in this annotation is from the Jan. 2007 (WUGSC 1.0/cb3) (cb3) 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.

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

References

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. PMID: 14500911; PMC: PMC208784

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961