New RepeatMasker Display

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Daniel Schmelter

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Oct 6, 2022, 1:32:08 PM10/6/22
to genome-...@soe.ucsc.edu

Hello Genomics Community,

We are happy to report that we've added a new data format and visualization style for genomic repeats, the bigRmsk format. This new format is highly flexible across different viewing ranges and is an information-rich way to display information from the RepeatMasker program. We currently have these computed tracks available on 2000+ genomes, including our GenArk assembly hubs. This format interfaces with all of our standard tools including Table Browser, API, and bigBed utility programs. More information, including examples, can be found on the track format description page below:

http://genome.ucsc.edu/goldenPath/help/bigRmsk.html

Diving into the new data format, this bigRmsk format (RepeatMasker) displays the type of repeat, location, orientation, alignment score, base-by-base alignment, insertion positions, and deletion information. The following example shows an annotation in left-pointing, reverse orientation, with an orange outline indicating a LINE element, a light grey filling showing a low-alignment score, split by an insertion indicated by the central join-line and with a dotted-line unaligned region on the left 3' end.

We hope this new format serves the community well! We give our thanks to the people who made this possible, namely Robert Hubley at the Institute of Systems Biology as well as Mark Diekans and Daniel Schmelter from UC Santa Cruz.

Daniel Schmelter
UCSC Genome Browser

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