Drosophila Chain/Net Track Settings

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

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All	*Clade*	Sophophora
*Subgenus*
melanogaster

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

Description

Genomic scaffolds from each Drosophila species are aligned against the D. simulans genome assembly (DsimGB2) 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.