Schema for Chain/Net - Chain and Net Alignments
  Database: mm39    Primary Table: chainGCF_003668045.3 Data last updated: 2020-12-08
Big Bed File Download: /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3.bb
Item Count: 7,770,374
Format description: bigChain pairwise alignment
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart112682867Start position in chromosome
chromEnd194901510End position in chromosome
name7Name or ID of item, ideally both human readable and unique
score1000Score (0-1000)
strand-+ or - for strand
tSize195154279size of target sequence
qNameNC_048598.1name of query sequence
qSize193770019size of query sequence
qStart122515221start of alignment on query sequence
qEnd193679796end of alignment on query sequence
chainScore2375087870score from chain

Sample Rows
 
chromchromStartchromEndnamescorestrandtSizeqNameqSizeqStartqEndchainScore
chr111268286719490151071000-195154279NC_048598.11937700191225152211936797962375087870
chr113011334413011363965739851000+195154279NW_023276806.12756981591909246821909249634991
chr113011640213011699011134991000-195154279NC_048597.123109786821292199421292250424524
chr11301236861301253182298411000-195154279NC_048598.1193770019243691992437082677723
chr11301237081301252652051211000+195154279NC_048601.199554469581105855811581682521
chr113012380013012420628101351000-195154279NC_048599.115561187014073282314073324013894
chr113012508913012525761844361000-195154279NC_048598.11937700191214689231214690795629
chr113012549413012569950410911000+195154279NC_048595.14616201173712976053712978197921
chr113016522513016542561555751000-195154279NC_048595.146162011726548635265488515679
chr113016525413016558156366751000+195154279NW_023276806.127569815987671104876714506644

Chain/Net (mm39ChainNet) Track Description
 

Description

Chain Track

The chain track shows alignments of mouse (Jun. 2020 (GRCm39/mm39)/mm39) 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 Jun. 2020 (GRCm39/mm39) (mm39) 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

The lastz 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.

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 was developed by: Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

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