Mouse Chain/Net Track Settings
 
Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments   (All Comparative Genomics tracks)

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 Chain  Mouse (Jun. 2020 (GRCm39/mm39)) Chained Alignments   Schema 
 
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 Chain  Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Chained Alignments   Schema 
 
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 Chain  Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Chained Alignments   Schema 
 
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 Chain  Mouse (Jun. 2020 (GRCm39/mm39)) Lift Over Chained Alignments   Schema 
 
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 Net  Mouse (Jun. 2020 (GRCm39/mm39)) Net Alignment   Schema 
 
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 Net  Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Net Alignment   Schema 
 
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Description

This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns.

Chain Track

The chain track shows alignments of Mouse/(Jun. 2020 (GRCm39/mm39)) to the Chinese hamster/Cricetulus griseus/GCF_003668045.3/2020-06-11 genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both Mouse and Chinese hamster 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 Mouse assembly or an insertion in the Chinese hamster 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 Chinese hamster 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/Chinese hamster chain for every part of the Chinese hamster genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The Mouse sequence used in this annotation is from the Jun. 2020 (GRCm39/mm39) assembly.

Display Conventions and Configuration

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

At base level in full display mode, this track will show the sequence of Mouse as it aligned to Chinese hamster. When the view is too large to show such detail, a graph of the alignment score will be shown.

Methods

Chain track

The Mouse genome was aligned to Chinese hamster genome with lastz. 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 Chinese hamster chromosome 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.

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.

The resulting net file was converted to axt format via netToAxt, then converted to maf format via axtToMaf, then converted to the bigMaf format with mafToBigMaf and bedToBigBed

Credits

lastz was developed by Robert Harris, Pennsylvania State University.

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

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University

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