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

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 All Clade brachycera  nematocera  holometabola 
D. simulans 
D. simulans 
D. sechellia 
D. yakuba 
D. erecta 
D. takahashii 
D. elegans 
D. eugracilis 
D. biarmipes 
D. rhopaloa 
D. ficusphila 
D. suzukii 
D. kikkawai 
D serrata 
D. ananassae 
D. bipectinata 
D obscura 
D. pseudoobscura 
D. miranda 
D. persimilis 
D subobscura 
D athabasca 
D. virilis 
D. willistoni 
D. grimshawi 
D. mojavensis 
D pseudoobscura 1 
D novamexicana 
D hydei 
D americana 
D montana 
D. albomicans 
Scaptodrosophila lebanonensis 
D busckii 
D arizonae 
D nasuta 
Zaprionus indianus 
D navojoa 
Phortica variegata 
Teleopsis dalmanni 
Rhagoletis zephyria 
Lucilia cuprina 
Bactrocera latifrons 
Bactrocera oleae 
Zeugodacus cucurbitae 
Phormia regina 
Ceratitis capitata 
Paykullia maculata 
Bactrocera tryoni 
M. domestica 
Bactrocera dorsalis 
Stomoxys calcitrans 
Glossina pallidipes 
Glossina fuscipes 
Glossina brevipalpis 
Glossina morsitans 2 
Glossina austeni 
Glossina palpalis gambiensis 
Ephydra gracilis 
Lucilia sericata 
Glossina morsitans 1 
Calliphora vicina 
Sphyracephala brevicornis 
Proctacanthus coquilletti 
Haematobia irritans 
Themira minor 
Megaselia abdita 
Tephritis californica 
Cirrula hians 
Hermetia illucens 
Neobellieria bullata 
Eutreta diana 
Holcocephala fusca 
Sarcophagidae BV 2014 
Liriomyza trifolii 
Eristalis dimidiata 
Condylostylus patibulatus 
Megaselia scalaris 
Trupanea jonesi 
Aedes albopictus 
Aedes aegypti 
A. gambiae 
A. gambiae 
Culex quinquefasciatus 
A maculatus 
A merus 
A dirus 
A arabiensis 
A sinensis 
A atroparvus 
A epiroticus 
A quadriannulatus 
A farauti 
A minimus 
A funestus 
A melas 
A coluzzii 
Clogmia albipunctata 
Phlebotomus papatasi 
A culicifacies 
A stephensi 
Coboldia fuscipes 
Culicoides sonorensis 
A albimanus 
A christyi 
A cracens 
A aquasalis 
Mochlonyx cinctipes 
A darlingi 
A farauti No4 
Lutzomyia longipalpis 
A koliensis 
Belgica antarctica 
A punctulatus 
Clunio marinus 
Mayetiola destructor 
Chironomus tentans 
Chironomus riparius 
A gambiae 1 
A nili 
Chaoborus trivitattus 
Tipula oleracea 
Trichoceridae BV 2014 
T. castaneum 
A. mellifera 
 All Clade brachycera  nematocera  holometabola 
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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 D. melanogaster 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 D. melanogaster 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 D. melanogaster 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 D. melanogaster 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/D. melanogaster chain for every part of the D. melanogaster 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.


Chain track

Transposons that have been inserted since the query sequence/D. melanogaster 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 D. melanogaster 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:


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.


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