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

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melanogaster 
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 Configure 		 D. mauritiana Net  D. mauritiana (Apr. 2020 (UC Irvine ASM438214v1/DmauRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. sechellia Net  D. sechellia (Feb. 2020 (UC Irvine ASM438219v1/DsecRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. simulans Net  D. simulans (Oct. 2021 (Princeton Prin_Dsim_3.1/DsimRefSeq3)) Alignment Net   Schema 
 
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 Configure 		 D. yakuba Net  D. yakuba (Aug. 2021 (Princeton Prin_Dyak_Tai18E2_2.1/DyakRefSeq3)) Alignment Net   Schema 
 
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 Configure 		 D. santomea Net  D. santomea (Sep. 2021 (Princeton Prin_Dsan_1.1/DsanRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. teissieri Net  D. teissieri (Sep. 2021 (Princeton Prin_Dtei_1.1/DteiRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. erecta Net  D. erecta (Oct. 2018 (AGI DereRS2/DereRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. ficusphila Net  D. ficusphila (Aug. 2021 (Stanford ASM1815226v1/DficRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. suzukii Net  D. suzukii (Oct. 2020 (IBDM LBDM_Dsuz_2.1.pri/DsuzRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. subpulchrella Net  D. subpulchrella (Nov. 2020 (Rockefeller RU_Dsub_v1.1/DspuRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. biarmipes Net  D. biarmipes (Sep. 2021 (Stanford ASM1814893v1/DbiaRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. takahashii Net  D. takahashii (Oct. 2021 (Stanford ASM1815269v1/DtakRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. eugracilis Net  D. eugracilis (May 2021 (Stanford ASM1815383v1/DeugRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. rhopaloa Net  D. rhopaloa (Oct. 2021 (Stanford ASM1815211v1/DrhoRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. elegans Net  D. elegans (May 2021 (Stanford ASM1815250v1/DeleRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. kikkawai Net  D. kikkawai (May 2021 (Stanford ASM1815253v1/DkikRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. serrata Net  D. serrata (May 2017 (University of Queensland Dser1.0/DserRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. bipectinata Net  D. bipectinata (Aug. 2021 (Stanford ASM1815384v1/DbipRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. ananassae Net  D. ananassae (Sep. 2021 (University of Maryland ASM1763931v2/DanaRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. pseudoobscura Net  D. pseudoobscura (Apr. 2020 (UC Irvine UCI_Dpse_MV25/DpseRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. persimilis Net  D. persimilis (Oct. 2018 (AGI DperRS2/DperRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. miranda Net  D. miranda (Apr. 2020 (UC Berkeley D.miranda_PacBio2.1/DmirRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. guanche Net  D. guanche (May 2020 (CNAG DGUA_6/DguaRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. subobscura Net  D. subobscura (June 2020 (UC Berkeley UCBerk_Dsub_1.0/DsobRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. obscura Net  D. obscura (May 2021 (Stanford ASM1815110v1/DobsRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. willistoni Net  D. willistoni (Feb. 2022 (UCI_dwil_1.1/DwilRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. arizonae Net  D. arizonae (Aug. 2016 (UNAM ASM165402v1/DariRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. mojavensis Net  D. mojavensis (Sep. 2021 (Stanford ASM1815372v1/DmojRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. navojoa Net  D. navojoa (Aug. 2019 (UNAM UFRJ_Dnav_4.2/DnavRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. hydei Net  D. hydei (Aug. 2019 (AGI DhydRS2/DhydRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. virilis Net  D. virilis (Feb. 2020 (AGI DvirRS2/DvirRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. novamexicana Net  D. novamexicana (Aug. 2019 (AGI DnovRS2.1/DnovRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. albomicans Net  D. albomicans (May 2020 (UC Berkeley drosAlbom15112-1751.03v1/DalbRefSeq1)) Alignment Net   Schema 
 
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 Configure 		 D. grimshawi Net  D. grimshawi (Aug. 2021 (Stanford ASM1815329v1/DgriRefSeq2)) Alignment Net   Schema 
 
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 Configure 		 D. busckii Net  D. busckii (Mar. 2020 (Max Planck Institute ASM1175060v1/DbusRefSeq1)) 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

Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110.

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. doi: 10.1073/pnas.1932072100.