Drosophila Chain/Net Track Settings

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

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All	*Clade*	Sophophora	Drosophila
*Subgenus*
melanogaster
repleta
virilis
grimshawi

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	hide Configure	D. melanogaster Chain	D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Chained Alignments	Schema
	hide Configure	D. melanogaster Net	D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) 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

Description

Genomic scaffolds from each Drosophila species are aligned against the D. mojavensis genome assembly (DmojCAF1) 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.