Subtracks⇓  Description⇓  Drosophila Chain/Net Track Settings
 
Drosophila Genomes, Chain and Net Alignments   (All Comparative Genomics tracks)

Maximum display mode:       Reset to defaults   
Select views (Help):
Chains ▾       Nets ▾      
Select subtracks by clade and subgenus:
 All Clade Sophophora  Drosophila  Dorsilopha 
Subgenus
melanogaster 
obscura 
willistoni 
repleta 
virilis 
grimshawi 
busckii 
  Top⇑
List subtracks: only selected/visible    all    (60 of 60 selected)  
 
hide
 Configure
 D. simulans Chain  D. simulans (May 2017 (Princeton ASM75419v2/DsimGB2)) Chained Alignments   Schema 
 
hide
 Configure
 D. simulans Net  D. simulans (May 2017 (Princeton ASM75419v2/DsimGB2)) Alignment Net   Schema 
 
hide
 Configure
 D. sechellia Chain  D. sechellia (May 2011 (Broad dsec_caf1/DsecCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. sechellia Net  D. sechellia (May 2011 (Broad dsec_caf1/DsecCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. yakuba Chain  D. yakuba (May 2011 (WUGSC dyak_caf1/DyakCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. yakuba Net  D. yakuba (May 2011 (WUGSC dyak_caf1/DyakCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. erecta Chain  D. erecta (May 2011 (Agencourt dere_caf1/DereCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. erecta Net  D. erecta (May 2011 (Agencourt dere_caf1/DereCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. eugracilis Chain  D. eugracilis (Apr. 2013 (BCM-HGSC/Deug_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. eugracilis Net  D. eugracilis (Apr. 2013 (BCM-HGSC/Deug_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. biarmipes Chain  D. biarmipes (Apr. 2013 (BCM-HGSC/Dbia_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. biarmipes Net  D. biarmipes (Apr. 2013 (BCM-HGSC/Dbia_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. suzukii Chain  D. suzukii (Sep. 2013 (BGI/Dsuz_1.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. suzukii Net  D. suzukii (Sep. 2013 (BGI/Dsuz_1.0)) Alignment Net   Schema 
 
hide
 Configure
 D. takahashii Chain  D. takahashii (Apr. 2013 (BCM-HGSC/Dtak_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. takahashii Net  D. takahashii (Apr. 2013 (BCM-HGSC/Dtak_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. elegans Chain  D. elegans (Apr. 2013 (BCM-HGSC/Dele_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. elegans Net  D. elegans (Apr. 2013 (BCM-HGSC/Dele_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. rhopaloa Chain  D. rhopaloa (Apr. 2013 (BCM-HGSC/Drho_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. rhopaloa Net  D. rhopaloa (Apr. 2013 (BCM-HGSC/Drho_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. ficusphila Chain  D. ficusphila (Apr. 2013 (BCM-HGSC/Dfic_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. ficusphila Net  D. ficusphila (Apr. 2013 (BCM-HGSC/Dfic_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. kikkawai Chain  D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. kikkawai Net  D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. serrata Chain  D. serrata (Apr. 2017 (University of Queensland Dser1.0/DserGB1)) Chained Alignments   Schema 
 
hide
 Configure
 D. serrata Net  D. serrata (Apr. 2017 (University of Queensland Dser1.0/DserGB1)) Alignment Net   Schema 
 
hide
 Configure
 D. ananassae Chain  D. ananassae (May 2011 (Agencourt dana_caf1/DanaCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. ananassae Net  D. ananassae (May 2011 (Agencourt dana_caf1/DanaCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. ananassae Chain  D. ananassae (Oct. 2015 (GEP/DanaImproved)) Chained Alignments   Schema 
 
hide
 Configure
 D. ananassae Net  D. ananassae (Oct. 2015 (GEP/DanaImproved)) Alignment Net   Schema 
 
hide
 Configure
 D. bipectinata Chain  D. bipectinata (Apr. 2013 (BCM-HGSC/Dbip_2.0)) Chained Alignments   Schema 
 
hide
 Configure
 D. bipectinata Net  D. bipectinata (Apr. 2013 (BCM-HGSC/Dbip_2.0)) Alignment Net   Schema 
 
hide
 Configure
 D. obscura Chain  D. obscura (July 2017 (NIG Dobs_1.0/DobsGB1)) Chained Alignments   Schema 
 
hide
 Configure
 D. obscura Net  D. obscura (July 2017 (NIG Dobs_1.0/DobsGB1)) Alignment Net   Schema 
 
hide
 Configure
 D. pseudoobscura Chain  D. pseudoobscura (Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3)) Chained Alignments   Schema 
 
hide
 Configure
 D. pseudoobscura Net  D. pseudoobscura (Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3)) Alignment Net   Schema 
 
hide
 Configure
 D. persimilis Chain  D. persimilis (May 2011 (Broad dper_caf1/DperCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. persimilis Net  D. persimilis (May 2011 (Broad dper_caf1/DperCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. miranda Chain  D. miranda (Apr. 2013 (UC Berkeley DroMir_2.2/DmirGB2)) Chained Alignments   Schema 
 
hide
 Configure
 D. miranda Net  D. miranda (Apr. 2013 (UC Berkeley DroMir_2.2/DmirGB2)) Alignment Net   Schema 
 
hide
 Configure
 D. willistoni Chain  D. willistoni (May 2011 (JCVI dwil_caf1/DwilCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. willistoni Net  D. willistoni (May 2011 (JCVI dwil_caf1/DwilCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. mojavensis Chain  D. mojavensis (May 2011 (Agencourt dmoj_caf1/DmojCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. mojavensis Net  D. mojavensis (May 2011 (Agencourt dmoj_caf1/DmojCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. mojavensis Chain  D. mojavensis (Apr. 2014 (GEP/DmojImproved)) Chained Alignments   Schema 
 
hide
 Configure
 D. mojavensis Net  D. mojavensis (Apr. 2014 (GEP/DmojImproved)) Alignment Net   Schema 
 
hide
 Configure
 D. arizonae Chain  D. arizonae (June 2016 (UNAM ASM165402v1/DariGB1)) Chained Alignments   Schema 
 
hide
 Configure
 D. arizonae Net  D. arizonae (June 2016 (UNAM ASM165402v1/DariGB1)) Alignment Net   Schema 
 
hide
 Configure
 D. navojoa Chain  D. navojoa (June 2016 (UNAM ASM165401v1/DnavGB1)) Chained Alignments   Schema 
 
hide
 Configure
 D. navojoa Net  D. navojoa (June 2016 (UNAM ASM165401v1/DnavGB1)) Alignment Net   Schema 
 
hide
 Configure
 D. hydei Chain  D. hydei (Nov. 2017 (UC Davis ASM278046v1/DhydGB1)) Chained Alignments   Schema 
 
hide
 Configure
 D. hydei Net  D. hydei (Nov. 2017 (UC Davis ASM278046v1/DhydGB1)) Alignment Net   Schema 
 
hide
 Configure
 D. virilis Chain  D. virilis (Sep. 2011 (Agencourt dvir_caf1/DvirCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. virilis Net  D. virilis (Sep. 2011 (Agencourt dvir_caf1/DvirCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. grimshawi Chain  D. grimshawi (May 2011 (Agencourt dgri_caf1/DgriCAF1)) Chained Alignments   Schema 
 
hide
 Configure
 D. grimshawi Net  D. grimshawi (May 2011 (Agencourt dgri_caf1/DgriCAF1)) Alignment Net   Schema 
 
hide
 Configure
 D. grimshawi Chain  D. grimshawi (Apr. 2014 (GEP/DgriImproved)) Chained Alignments   Schema 
 
hide
 Configure
 D. grimshawi Net  D. grimshawi (Apr. 2014 (GEP/DgriImproved)) Alignment Net   Schema 
 
hide
 Configure
 D. busckii Chain  D. busckii (Sep. 2015 (UC Berkeley ASM127793v1/DbusGB1)) Chained Alignments   Schema 
 
hide
 Configure
 D. busckii Net  D. busckii (Sep. 2015 (UC Berkeley ASM127793v1/DbusGB1)) Alignment Net   Schema 
    60 of 60 selected

Description

Genomic scaffolds from each Drosophila species are aligned against the D. melanogaster genome assembly (dm6) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting).

References

Chain/Net

Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489.

LAST

Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

  Top⇑ 
  Top⇑