-The Alignment Differences track shows mismatches and indels between the assembly from which the -track was QuickLifted and the current genome. +The Alignment Differences track shows mismatches, insertions, deletions, and double-sided +insertions between two assemblies. In QuickLift, the +source assembly is the assembly where the annotations come from, and the +destination (target) assembly is the assembly you are currently viewing. +QuickLift maps (liftOver) annotations on demand from the source +to the target using whole-genome alignment chains.
-Visible tracks, custom tracks, and track hubs on the Browser graphic page are carried over (lifted) -to the new assembly using the QuickLift tracks checkbox. When a single -track from a container track, such as a superTrack or composite, is lifted, the entire container -track is carried over to the new assembly. +This track is part of the QuickLift track group, which appears +under a green "QuickLift from ..." group in the target +genome assembly. QuickLift tracks have a green left-side button +bar in the Browser graphic, instead of the usual gray, and can be removed by the + button.
-QuickLift tracks appear under a green -"QuickLift from ..." group in the New assembly. -QuickLift tracks can be removed by the - button. QuickLift tracks have a green -left-side button bar in the Browser graphic, instead of the usual gray. -
--The "Alignment Differences" track displays liftOver differences using triangles and -lines; mousing over a triangle displays base-pair (bp) information. Lines and triangles are -color-coded as follows: +The Alignment Differences track displays liftOver differences using triangles and +lines. Alignment differences are marked by lines, with colored triangles indicating the type of +difference:
Clicking a triangle provides additional information about the alignment.
++Mousing over a triangle displays the size base-pair (bp) difference and the type of alignment +difference. Clicking a triangle opens a details page showing: +
+
+An alignment between two DNA sequences maps every nucleotide in one sequence to a nucleotide in another sequence. By making and using whole-genome alignments (Kent et al., 2003), genome annotations can be "lifted" to another assembly -(LiftOver) in bulk, one track at a time. -QuickLift is a tool that uses the same algorithm, but it maps -("liftOver") annotations on demand, in real-time, for all visible tracks. Only the -annotations in the currently visible region are lifted, so this is usually fast enough when -browsing a genome. +(liftOver) in bulk, one track at a time. +QuickLift uses the same algorithm to lift annotations on demand, in +real-time, for all visible tracks. Only the annotations in the currently visible region are lifted, +so this is usually fast enough when browsing a genome. +
+ ++The Alignment Differences track is generated by comparing the whole-genome alignment chain between +the source and target assemblies. Where the alignment differs, the track classifies each +difference by type:
+QuickLift functionality depends on the availability of alignment files (chains) that describe how sequences in one assembly correspond to another. The alignment files are -currently made at UCSC, but we are working on making the pipeline to align two genomes more widely -available. +currently made at UCSC, and if no alignment file is available for the assembly in which you're +interested, please send a request to the genome mailing list, and we will attempt to provide you with one.
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. PMID: 14500911; PMC: PMC208784