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

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 Configure 		 D. simulans Chain  D. simulans (May 2017 (Princeton ASM75419v2/DsimGB2)) Chained Alignments   Schema 
 
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 Configure 		 D. simulans Net  D. simulans (May 2017 (Princeton ASM75419v2/DsimGB2)) Alignment Net   Schema 
 
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 Configure 		 D. sechellia Chain  D. sechellia (May 2011 (Broad dsec_caf1/DsecCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. sechellia Net  D. sechellia (May 2011 (Broad dsec_caf1/DsecCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. yakuba Chain  D. yakuba (May 2011 (WUGSC dyak_caf1/DyakCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. yakuba Net  D. yakuba (May 2011 (WUGSC dyak_caf1/DyakCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. erecta Chain  D. erecta (May 2011 (Agencourt dere_caf1/DereCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. erecta Net  D. erecta (May 2011 (Agencourt dere_caf1/DereCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. eugracilis Chain  D. eugracilis (Apr. 2013 (BCM-HGSC/Deug_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. eugracilis Net  D. eugracilis (Apr. 2013 (BCM-HGSC/Deug_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. biarmipes Chain  D. biarmipes (Apr. 2013 (BCM-HGSC/Dbia_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. biarmipes Net  D. biarmipes (Apr. 2013 (BCM-HGSC/Dbia_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. suzukii Chain  D. suzukii (Sep. 2013 (BGI/Dsuz_1.0)) Chained Alignments   Schema 
 
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 Configure 		 D. suzukii Net  D. suzukii (Sep. 2013 (BGI/Dsuz_1.0)) Alignment Net   Schema 
 
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 Configure 		 D. takahashii Chain  D. takahashii (Apr. 2013 (BCM-HGSC/Dtak_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. takahashii Net  D. takahashii (Apr. 2013 (BCM-HGSC/Dtak_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. elegans Chain  D. elegans (Apr. 2013 (BCM-HGSC/Dele_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. elegans Net  D. elegans (Apr. 2013 (BCM-HGSC/Dele_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. rhopaloa Chain  D. rhopaloa (Apr. 2013 (BCM-HGSC/Drho_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. rhopaloa Net  D. rhopaloa (Apr. 2013 (BCM-HGSC/Drho_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. ficusphila Chain  D. ficusphila (Apr. 2013 (BCM-HGSC/Dfic_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. ficusphila Net  D. ficusphila (Apr. 2013 (BCM-HGSC/Dfic_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. kikkawai Chain  D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. kikkawai Net  D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. serrata Chain  D. serrata (Apr. 2017 (University of Queensland Dser1.0/DserGB1)) Chained Alignments   Schema 
 
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 Configure 		 D. serrata Net  D. serrata (Apr. 2017 (University of Queensland Dser1.0/DserGB1)) Alignment Net   Schema 
 
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 Configure 		 D. ananassae Chain  D. ananassae (May 2011 (Agencourt dana_caf1/DanaCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. ananassae Net  D. ananassae (May 2011 (Agencourt dana_caf1/DanaCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. ananassae Chain  D. ananassae (Oct. 2015 (GEP/DanaImproved)) Chained Alignments   Schema 
 
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 Configure 		 D. ananassae Net  D. ananassae (Oct. 2015 (GEP/DanaImproved)) Alignment Net   Schema 
 
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 Configure 		 D. bipectinata Chain  D. bipectinata (Apr. 2013 (BCM-HGSC/Dbip_2.0)) Chained Alignments   Schema 
 
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 Configure 		 D. bipectinata Net  D. bipectinata (Apr. 2013 (BCM-HGSC/Dbip_2.0)) Alignment Net   Schema 
 
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 Configure 		 D. obscura Chain  D. obscura (July 2017 (NIG Dobs_1.0/DobsGB1)) Chained Alignments   Schema 
 
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 Configure 		 D. obscura Net  D. obscura (July 2017 (NIG Dobs_1.0/DobsGB1)) Alignment Net   Schema 
 
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 Configure 		 D. pseudoobscura Chain  D. pseudoobscura (Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3)) Chained Alignments   Schema 
 
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 Configure 		 D. pseudoobscura Net  D. pseudoobscura (Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3)) Alignment Net   Schema 
 
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 Configure 		 D. persimilis Chain  D. persimilis (May 2011 (Broad dper_caf1/DperCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. persimilis Net  D. persimilis (May 2011 (Broad dper_caf1/DperCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. miranda Chain  D. miranda (Apr. 2013 (UC Berkeley DroMir_2.2/DmirGB2)) Chained Alignments   Schema 
 
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 Configure 		 D. miranda Net  D. miranda (Apr. 2013 (UC Berkeley DroMir_2.2/DmirGB2)) Alignment Net   Schema 
 
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 Configure 		 D. willistoni Chain  D. willistoni (May 2011 (JCVI dwil_caf1/DwilCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. willistoni Net  D. willistoni (May 2011 (JCVI dwil_caf1/DwilCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. mojavensis Chain  D. mojavensis (May 2011 (Agencourt dmoj_caf1/DmojCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. mojavensis Net  D. mojavensis (May 2011 (Agencourt dmoj_caf1/DmojCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. mojavensis Chain  D. mojavensis (Apr. 2014 (GEP/DmojImproved)) Chained Alignments   Schema 
 
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 Configure 		 D. mojavensis Net  D. mojavensis (Apr. 2014 (GEP/DmojImproved)) Alignment Net   Schema 
 
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 Configure 		 D. arizonae Chain  D. arizonae (June 2016 (UNAM ASM165402v1/DariGB1)) Chained Alignments   Schema 
 
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 Configure 		 D. arizonae Net  D. arizonae (June 2016 (UNAM ASM165402v1/DariGB1)) Alignment Net   Schema 
 
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 Configure 		 D. navojoa Chain  D. navojoa (June 2016 (UNAM ASM165401v1/DnavGB1)) Chained Alignments   Schema 
 
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 Configure 		 D. navojoa Net  D. navojoa (June 2016 (UNAM ASM165401v1/DnavGB1)) Alignment Net   Schema 
 
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 Configure 		 D. hydei Chain  D. hydei (Nov. 2017 (UC Davis ASM278046v1/DhydGB1)) Chained Alignments   Schema 
 
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 Configure 		 D. hydei Net  D. hydei (Nov. 2017 (UC Davis ASM278046v1/DhydGB1)) Alignment Net   Schema 
 
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 Configure 		 D. virilis Chain  D. virilis (Sep. 2011 (Agencourt dvir_caf1/DvirCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. virilis Net  D. virilis (Sep. 2011 (Agencourt dvir_caf1/DvirCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. grimshawi Chain  D. grimshawi (May 2011 (Agencourt dgri_caf1/DgriCAF1)) Chained Alignments   Schema 
 
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 Configure 		 D. grimshawi Net  D. grimshawi (May 2011 (Agencourt dgri_caf1/DgriCAF1)) Alignment Net   Schema 
 
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 Configure 		 D. grimshawi Chain  D. grimshawi (Apr. 2014 (GEP/DgriImproved)) Chained Alignments   Schema 
 
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 Configure 		 D. grimshawi Net  D. grimshawi (Apr. 2014 (GEP/DgriImproved)) Alignment Net   Schema 
 
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 Configure 		 D. busckii Chain  D. busckii (Sep. 2015 (UC Berkeley ASM127793v1/DbusGB1)) Chained Alignments   Schema 
 
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 Configure 		 D. busckii Net  D. busckii (Sep. 2015 (UC Berkeley ASM127793v1/DbusGB1)) Alignment Net   Schema 
    

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.