UCSC Browser Track for D. simulans w501

Supporting data from "Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans" (Rogers et al. 2014, MBE) is available for download here.

Supplementary data files include lists of tandem duplications and associated gene fragements, as well as Bed formatted files describing segregating tandem duplications for use in the UCSC genome browser. To view regions with annotated genes as well as regions with segregating derived tandem duplications:

• At UCSC genome browser click on MyData-> TrackHubs -> PublicHubs
• Check "ThorntonHub"
• In the genome browser under "group" look for ThorntonHub. "Andolfatto w501 D. simulans reference assembly" for the current genome release.

The hub comes with automatically configured tracks displaying the span of polymorphic tandem duplications, CDS annotations, and transcript annotations. Transcript names in the form of CG1111-PX can be searched by name, but the transcript identifier (PA, PB, PC...) is required. You may also search the text of the annotations bed file to find chromosome coordinates for your gene of interest.

Manuscripts using variant calls for tandem duplications should cite our manuscript in MBE. Variants from D. simulans were defined using the w501 reference. and users should cite Hu et al. 2012. Users interested in uploading custom tracks for D. simulans w501 can contact Rebekah Rogers.

Data Set Download

Bed formatted files and other related datasets can be found at github