Schema for Vertebrate Chain/Net - Vertebrate Genomes, Chain and Net Alignments
  Database: mm10    Primary Table: chainMacEug2    Row Count: 4,045,168   Data last updated: 2012-03-24
Format description: Summary info about a chain of alignments
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 608smallint(5) unsigned Indexing field to speed chromosome range queries.
score 24816double score of chain
tName chr1varchar(255) Target sequence name
tSize 195471971int(10) unsigned Target sequence size
tStart 3094693int(10) unsigned Alignment start position in target
tEnd 3095760int(10) unsigned Alignment end position in target
qName GL133416varchar(255) Query sequence name
qSize 53989int(10) unsigned Query sequence size
qStrand -char(1) Query strand
qStart 33366int(10) unsigned Alignment start position in query
qEnd 34470int(10) unsigned Alignment end position in query
id 343185int(10) unsigned chain id

Connected Tables and Joining Fields
        mm10.chainMacEug2Link.chainId (via chainMacEug2.id)
      mm10.netMacEug2.chainId (via chainMacEug2.id)

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
60824816chr119547197130946933095760GL13341653989-3336634470343185
6088044chr119547197131347393134961GL1369888365+183020542553102
6097853chr119547197131468843147089GL13997813349-714673692599367
6098257chr119547197131468843147099GL095688131967-20733209712502139
6097859chr119547197131468993147043GL08226125059-932994992597852
60916282chr119547197131468993147256GL0459642260-85462867994
60938872chr119547197131997873216986GL136526122103-3318654220101295
60996341chr119547197132142463216723GL1452452467+1224674773
6095853chr119547197132160153216270ABQO010291211874+4927523148858
60928250chr119547197132160223217012GL13692744715+1975321012253466

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

Vertebrate Chain/Net (vertebrateChainNet) Track Description
 

Description

Chain Track

The chain track shows alignments of mouse (Dec. 2011 (GRCm38/mm10)/mm10) to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and the other genome 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 other assembly or an insertion in the mouse 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 other 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.

Net Track

The net track shows the best mouse/other chain for every part of the other genome. It is useful for finding orthologous regions and for studying genome rearrangement. The mouse sequence used in this annotation is from the Dec. 2011 (GRCm38/mm10) (mm10) assembly.

Display Conventions and Configuration

Multiple species are grouped together in a composite track. In the display and on the configuration page, an effort was made to group them loosely into "clades." These groupings are based on the taxonomic classification at NCBI, using the CommonTree tool. Some organisms may be pulled from a larger group into a subgroup, to emphasize a relationship. For example, members of an Order may be listed together, while other organisms in the same Superorder may be grouped separately under the Superorder name.

Chain Track

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.

Net Track

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

Chain track

Transposons that have been inserted since the mouse/other split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single chromosome from the other genome 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.

See also: lastz parameters and other details (e.g., update time) and chain minimum score and gap parameters used in these alignments.

Additional chain/net tracks added since the completion of the 60-way conservation set mentioned in these external document pages include:

  • Medium ground finch, geoFor1, April 2012, BGI,
    Chicken, galGal5, December 2015, ICGC,
    lastz alignment matrix:
     ACGT
    A91-90-25-100
    C-90100-100-25
    G-25-100100-90
    T-100-25-9091

    Chains scoring below a minimum score of '5000' were discarded, and the linear gap matrix used with axtChain:

    -linearGap=loose
    tablesize    11
    smallSize   111
    position  1   2   3   11  111  2111  12111  32111  72111  152111  252111
    qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600
    tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600
    bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000
    

Net track

Chains were derived from lastz 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

Lastz (previously known as 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 and nets were created by Robert Baertsch and Jim Kent.

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

References

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

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 RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961