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 
Subgenus
melanogaster 
List subtracks: only selected/visible    all  
 
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. yakuba genome assembly (DyakCAF1) 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.