Nematodes Chain/Net Track Settings
 
Nematodes Chain and Net Alignments   (All Comparative Genomics tracks)

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Select subtracks by clade and species:
 All Clade Rhabditina  Spirurina  Tylenchina  Strongylida  Plectida  Dorylaimia  Platyhelminthes  Deuterostomia 
Species
C nigoni 
C. remanei 
C briggsae 
C sp26 LS 2015 
C. brenneri 
C latens 
C. tropicalis 
C sp34 TK 2017 
C sp40 LS 2015 
C. japonica 
C sp39 LS 2015 
C sp38 MB 2015 
C sp31 LS 2015 
C. sp. 5 ju800 
C. angaria 
C. briggsae 
C sp32 LS 2015 
Diploscapter coronatus 
Diploscapter pachys 
C sp21 LS 2015 
Ancylostoma caninum 
Oscheius tipulae 
A. ceylanicum 
Parapristionchus giblindavisi 
Necator americanus 
Oscheius TEL 2014 
Ancylostoma duodenale 
Oesophagostomum dentatum 
Pristionchus arcanus 
Pristionchus pacificus 
Pristionchus maxplancki 
Pristionchus entomophagus 
Pristionchus exspectatus 
H. bacteriophora/m31e 
N. americanus 
Oscheius MCB 
P. pacificus 
P. exspectatus 
Onchocerca volvulus 
Wuchereria bancrofti 
Dirofilaria immitis 
Brugia pahangi 
Onchocerca ochengi 
Brugia malayi 
Loa loa 
Setaria digitata 
Onchocerca flexuosa 
Setaria equina 
Ascaris suum 
Parascaris univalens 
Toxocara canis 
Pig roundworm 
O. volvulus 
Filarial worm 
Eye worm 
Dog heartworm 
Elaeophora elaphi 
Threadworm 
Strongyloides stercoralis 
Strongyloides venezuelensis 
Meloidogyne arenaria 
Strongyloides papillosus 
Parastrongyloides trichosuri 
Meloidogyne incognita 
Meloidogyne javanica 
Acrobeloides nanus 
Rhabditophanes KR3021 
Meloidogyne graminicola 
Rotylenchulus reniformis 
Ditylenchus destructor 
Bursaphelenchus xylophilus 
Steinernema monticolum 
Meloidogyne floridensis 
Steinernema carpocapsae 
Steinernema scapterisci 
Steinernema feltiae 
Subanguina moxae 
Globodera ellingtonae 
Globodera rostochiensis 
Steinernema glaseri 
Globodera pallida 
Heterodera glycines 
Microworm 
Pine wood nematode 
M. hapla 
M. incognita 
Dictyocaulus viviparus 
Nippostrongylus brasiliensis 
Heligmosomoides polygyrus bakeri 
Teladorsagia circumcincta 
Haemonchus contortus 
Angiostrongylus cantonensis 
Barber pole worm 
Plectus sambesii 
Trichinella murrelli 
Trichinella zimbabwensis 
Trichinella pseudospiralis 
Trichinella papuae 
Trichinella T6 
Trichinella britovi 
Trichinella T8 
Trichinella T9 
Trichinella patagoniensis 
Trichinella nelsoni 
Trichinella nativa 
Trichinella spiralis 
Romanomermis culicivorax 
Trichuris trichiura 
Trichuris muris 
Whipworm 
Trichinella 
Schmidtea mediterranea 
Girardia tigrina 
Dugesia japonica 
Macrostomum lignano 
Schistosoma mansoni 
Schistosoma haematobium 
Schistosoma japonicum 
Gyrodactylus salaris 
Hymenolepis microstoma 
Fasciola hepatica 
Taenia multiceps 
Fasciola gigantica 
Taenia saginata 
Clonorchis sinensis 
Opisthorchis viverrini 
Echinococcus multilocularis 
Taenia asiatica 
Echinococcus canadensis 
Taenia solium 
Echinococcus granulosus 
Spirometra erinaceieuropaei 
Dicrocoelium dendriticum 
C. intestinalis 
Species
 All Clade Rhabditina  Spirurina  Tylenchina  Strongylida  Plectida  Dorylaimia  Platyhelminthes  Deuterostomia 
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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 a query genome sequence to the C. elegans genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both the query sequence and C. elegans 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 the query sequence assembly or an insertion in the C. elegans 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 C. elegans 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 query sequence/C. elegans chain for every part of the C. elegans genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement.

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.

Methods

Chain track

Transposons that have been inserted since the query sequence/C. elegans 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 query sequence chromosome and a single C. elegans 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. 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:

-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