Human Chain/Net Track Settings
 
Chain and Net alignments to target sequence: GCA_009914755.4_T2T-CHM13v2.0   (All Comparative Genomics tracks)

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Select subtracks by clade and species:
 All Clade human 
Species
GCA 021950905.1 
GCA 021951015.1 
hg19 
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  Species↓1 views↓2 Clade↓3   Track Name↓4  
 
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 GCA 021950905.1  Chains  human  HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Chained Alignments   Schema 
 
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 GCA 021950905.1  Nets  human  HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Net Alignment   Schema 
 
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 GCA 021950905.1  Chains  human  HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Syntenic Chained Alignments   Schema 
 
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 GCA 021950905.1  Nets  human  HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Syntenic Net Alignment   Schema 
 
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 GCA 021950905.1  Chains  human  HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Reciprocal Best Chained Alignments   Schema 
 
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 GCA 021950905.1  Nets  human  HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment   Schema 
 
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 GCA 021951015.1  Chains  human  HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Chained Alignments   Schema 
 
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 GCA 021951015.1  Nets  human  HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Net Alignment   Schema 
 
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 GCA 021951015.1  Chains  human  HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Chained Alignments   Schema 
 
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 GCA 021951015.1  Nets  human  HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Net Alignment   Schema 
 
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 GCA 021951015.1  Chains  human  HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Chained Alignments   Schema 
 
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 GCA 021951015.1  Nets  human  HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment   Schema 
 
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 hg19  Chains  human  hg19 (Feb. 2009) Chained Alignments   Schema 
 
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 hg19  Nets  human  hg19 (Feb. 2009) Net Alignment   Schema 
 
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 hg19  Chains  human  hg19 (Feb. 2009) Syntenic Chained Alignments   Schema 
 
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 hg19  Nets  human  hg19 (Feb. 2009) Syntenic Net Alignment   Schema 
 
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 hg19  Chains  human  hg19 (Feb. 2009) Reciprocal Best Chained Alignments   Schema 
 
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 hg19  Nets  human  hg19 (Feb. 2009) Reciprocal Best Net Alignment   Schema 
 
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 hg38  Chains  human  hg38 (Dec. 2013) Chained Alignments   Schema 
 
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 hg38  Nets  human  hg38 (Dec. 2013) Net Alignment   Schema 
 
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 hg38  Chains  human  hg38 (Dec. 2013) Syntenic Chained Alignments   Schema 
 
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 hg38  Nets  human  hg38 (Dec. 2013) Syntenic Net Alignment   Schema 
 
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 hg38  Chains  human  hg38 (Dec. 2013) Reciprocal Best Chained Alignments   Schema 
 
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 hg38  Nets  human  hg38 (Dec. 2013) Reciprocal Best Net Alignment   Schema 
    

Current issues

Please note, the color scheme on the chainNet tracks to the two human sequences HG002 paternal and maternal are currently not colored correctly. We are working on a fix to this issue. The color scheme for the chainNet tracks to the human sequences GRCh37/hg19 and GRCh38/hg38 are colored correctly.

Description

This track shows regions of this target genome (T2T-CHM13v2.0 - 2022-01-24) that has alignment to other query 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.

Other query genome assemblies aligning to this target genome assembly:

Each of the query genome alignments are represented in this display with four types of summaries, with two tracks for each type: a chain/net set.

  • complete pair-wise alignment before any filtering
  • syntenic net, the full alignment filtered for syntenic alignments only
  • reciprocal best, the full alignment filtered for reciprocal best alignments only
  • lift over, the full alignment filtered for the best target/query alignments only

Chain Track

The chain tracks shows alignments of the other genome assemblies to the T2T-CHM13v2.0/GCA_009914755.4/2022-01-24 genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both query and target geomes 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 query assembly or an insertion in the target 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 target 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 alignment of the best query/target chain for every part of the target genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement.

The kent command line program: chainNet is used to convert a chain alignment to the net representation of that alignment. This is a filter that eliminates low quality chains and accumulates chains in synteny together into one net representating that synteny block.

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 query as it aligned to target. When the view is too large to show such detail, a graph of the alignment score will be shown.

Methods

Chain track

The query genome was aligned to target 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 query chromosome and a single target 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