Vertebrate Chain/Net Track Settings
 
Vertebrate Genomes, Chain and Net Alignments   (All Comparative Genomics tracks)

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Select views (help):
Chains ▾       Nets ▾      
Select subtracks by clade and species:
 All Clade Mammalia  Aves  Euteleostomi  Teleostei  Percomorpha  Petromyzon 
Species
Wallaby 
Tasmanian devil 
Opossum 
Platypus 
Medium ground finch 
Budgerigar 
Zebra finch 
Chicken 
Turkey 
Goldlen eagle 
Lizard 
Turtle 
Frog 
Coelacanth 
Atlantic cod 
Zebrafish 
Stickleback 
Fugu 
Tetraodon 
Tilapia 
Medaka 
Lamprey 
Species
 All Clade Mammalia  Aves  Euteleostomi  Teleostei  Percomorpha  Petromyzon 
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  Species↓1 views↓2 Clade↓3   Track Name↓4  
 
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 Wallaby  Chains  Mammalia  Wallaby (Sep. 2009 (TWGS Meug_1.1/macEug2)) Chained Alignments   schema 
 
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 Wallaby  Nets  Mammalia  Wallaby (Sep. 2009 (TWGS Meug_1.1/macEug2)) Alignment Net   schema 
 
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 Tasmanian devil  Chains  Mammalia  Tasmanian devil (Feb. 2011 (WTSI Devil_ref v7.0/sarHar1)) Chained Alignments   schema 
 
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 Tasmanian devil  Nets  Mammalia  Tasmanian devil (Feb. 2011 (WTSI Devil_ref v7.0/sarHar1)) Alignment Net   schema 
 
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 Opossum  Chains  Mammalia  Opossum (Oct. 2006 (Broad/monDom5)) Chained Alignments   schema 
 
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 Opossum  Nets  Mammalia  Opossum (Oct. 2006 (Broad/monDom5)) Alignment Net   schema 
 
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 Platypus  Chains  Mammalia  Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Chained Alignments   schema 
 
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 Platypus  Nets  Mammalia  Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Alignment Net   schema 
 
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 Medium ground finch  Chains  Aves  Medium ground finch (Apr. 2012 (GeoFor_1.0/geoFor1)) Chained Alignments   schema 
 
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 Medium ground finch  Nets  Aves  Medium ground finch (Apr. 2012 (GeoFor_1.0/geoFor1)) Alignment Net   schema 
 
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 Budgerigar  Chains  Aves  Budgerigar (Sep. 2011 (WUSTL v6.3/melUnd1)) Chained Alignments   schema 
 
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 Budgerigar  Nets  Aves  Budgerigar (Sep. 2011 (WUSTL v6.3/melUnd1)) Alignment Net   schema 
 
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 Zebra finch  Nets  Aves  Zebra finch (Jul. 2008 (WUGSC 3.2.4/taeGut1)) Alignment Net   schema 
 
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 Goldlen eagle  Chains  Aves  Golden eagle (Oct. 2014 (aquChr-1.0.2/aquChr2)) Chained Alignments   schema 
 
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 Goldlen eagle  Nets  Aves  Golden eagle (Oct. 2014 (aquChr-1.0.2/aquChr2)) Alignment Net   schema 
 
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 Lizard  Nets  Euteleostomi  Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Alignment Net   schema 
 
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 Turtle  Nets  Euteleostomi  Painted turtle (Dec. 2011 (v3.0.1/chrPic1)) Alignment Net   schema 
 
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 Frog  Nets  Euteleostomi  African clawed frog (Aug. 2016 (Xenopus_laevis_v2/xenLae2)) Alignment Net   schema 
 
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 Frog  Nets  Euteleostomi  X. tropicalis (Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)) Alignment Net   schema 
 
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 Frog  Nets  Euteleostomi  X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Alignment Net   schema 
 
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 Atlantic cod  Nets  Teleostei  Atlantic cod (May 2010 (Genofisk GadMor_May2010/gadMor1)) Alignment Net   schema 
 
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 Zebrafish  Nets  Teleostei  Zebrafish (May 2017 (GRCz11/danRer11)) Alignment Net   schema 
 
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 Tetraodon  Nets  Percomorpha  Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Alignment Net   schema 
 
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 Tilapia  Nets  Percomorpha  Nile tilapia (Jan. 2011 (Broad oreNil1.1/oreNil2)) Alignment Net   schema 
 
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 Medaka  Nets  Percomorpha  Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Alignment Net   schema 
 
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 Lamprey  Nets  Petromyzon  Lamprey (Dec. 2017 (Pmar_germline 1.0/petMar3)) Alignment Net   schema 
    

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 mouse assembly or an insertion in the other 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