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

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 All Clade Hominidae  Cercopithecinae  Haplorrhini  Strepsirrhini 
Crab-eating macaque 
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  Species↓1 Views↓2 Clade↓3   Track Name↓4  
 Chimp  Chains  Hominidae  Chimp (May 2016 (Pan_tro 3.0/panTro5)) Chained Alignments   schema 
 Chimp  Nets  Hominidae  Chimp (May 2016 (Pan_tro 3.0/panTro5)) Alignment Net   schema 
 Bonobo  Chains  Hominidae  Bonobo (May 2012 (Max-Planck/panPan1)) Chained Alignments   schema 
 Bonobo  Nets  Hominidae  Bonobo (May 2012 (Max-Planck/panPan1)) Alignment Net   schema 
 Gorilla  Chains  Hominidae  Gorilla (Mar. 2016 (GSMRT3/gorGor5)) Chained Alignments   schema 
 Gorilla  Nets  Hominidae  Gorilla (Mar. 2016 (GSMRT3/gorGor5)) Alignment Net   schema 
 Orangutan  Chains  Hominidae  Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Chained Alignments   schema 
 Orangutan  Nets  Hominidae  Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Alignment Net   schema 
 Crab-eating macaque  Chains  Cercopithecinae  Crab-eating macaque (Jun. 2013 (Macaca_fascicularis_5.0/macFas5)) Chained Alignments   schema 
 Crab-eating macaque  Nets  Cercopithecinae  Crab-eating macaque (Jun. 2013 (Macaca_fascicularis_5.0/macFas5)) Alignment Net   schema 
 Rhesus  Chains  Cercopithecinae  Rhesus (Nov. 2015 (BCM Mmul_8.0.1/rheMac8)) Chained Alignments   schema 
 Rhesus  Nets  Cercopithecinae  Rhesus (Nov. 2015 (BCM Mmul_8.0.1/rheMac8)) Alignment Net   schema 
 Green Monkey  Chains  Cercopithecinae  Green monkey (Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2)) Chained Alignments   schema 
 Green Monkey  Nets  Cercopithecinae  Green monkey (Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2)) Alignment Net   schema 
 Proboscis monkey  Chains  Cercopithecinae  Proboscis monkey (Nov. 2014 (Charlie1.0/nasLar1)) Chained Alignments   schema 
 Proboscis monkey  Nets  Cercopithecinae  Proboscis monkey (Nov. 2014 (Charlie1.0/nasLar1)) Alignment Net   schema 
 Tarsier  Chains  Haplorrhini  Tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)) Chained Alignments   schema 
 Tarsier  Nets  Haplorrhini  Tarsier (Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)) Alignment Net   schema 
 Mouse lemur  Chains  Strepsirrhini  Mouse lemur (May 2015 (Mouse lemur/micMur2)) Chained Alignments   schema 
 Mouse lemur  Nets  Strepsirrhini  Mouse lemur (May 2015 (Mouse lemur/micMur2)) Alignment Net   schema 


Chain Track

The chain track shows alignments of human (Dec. 2013 (GRCh38/hg38)) 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 human 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 human 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 only the alignments from the highest-scoring chain for each region of the human genome assembly. It is useful for finding orthologous regions and for studying genome rearrangement. The human sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) 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

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.


Chain track

The assemblies were examined for any transposons that had been inserted since the divergence of the two species. Any such transposons were removed before running the alignment. The abbreviated genomes were aligned with lastz, and the removed transposons were then 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 human 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.

The lastz matrices used for these alignments can be found in our download directory for the Dec. 2013 (GRCh38/hg38) assembly. See the README.txt file within the relevant vsAssembly directory for details (e.g., parameters for the alignment with tarSyr2 can be found in the vsTarSyr2/ subdirectory).

For the alignments to Chimp and Rhesus, chains scoring below a minimum score of '5000' were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain:


tableSize    11
smallSize   111
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300
For the alignments to Tarsier and Bonobo, chains scoring below a minimum score of '3000' were discarded; the remaining chains are displayed in this track. The same linear gap matrix shown above was used with axtChain.

Chains for low-coverage assemblies for which no browser has been built are not available as browser tracks, but only from our downloads page.

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.


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.


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