biowu/transposons

Drosophila transposable element consensus sequences

TRANSPOSON SEQUENCE CANONICAL SETS FOR DROSOPHILA

This repository contains 'canonical' DNA sequences of the transposable elements from species in the genus Drosophila.

History: These sequences were originally compiled by Takis Benos (EBI), Leyla Bayraktaroglu (Harvard) and Michael Ashburner (EBI & Cambridge) with help from Aubrey de Grey (Cambridge), Joe Chillemi (Harvard) and Martin Reese (LBNL). We thank Suzi Lewis (Berkeley) for inspiration and discussion, Guochun Liao (Berkeley) for his repeat sequence set and newly discovered transposable element sequences from the Berkeley P1 clones, and Lynn Crosby (Harvard) for her annotations of some elements.

Subsequent curation of these sequences has been in the context of the Drosophila Genome Project and was a collaboration between M. Ashburner (Cambridge), Josh Kaminker (Berkeley) and Casey Bergman (Berkeley). From Version 8.0 this set has been maintained by Michael Ashburner and Casey Bergman in Cambridge. The last version updated by Michael Ashburner was Version 9.411 and is available here. FlyBase made minor modifications to Version 9.411 to generate version 9.42 in 2009, which is the most recent release available at FlyBase.

From version v9.43 onwards, this dataset has been maintained under continuous version control by Casey Bergman (Manchester) at: https://github.com/cbergman/transposons/. Contributions are welcome by submitting pull requests or opening issues for this repository. For pull requests, please make suggested edits to the files in the "current" directory. These contributions will be reviewed and, if merged, will be used to make an incremented version of the dataset in the "releases" directory.

The major changes from version 9.42 to 9.43 are to separate the metadata into a separarte README file and add TART-A, TART-B, and TART-C DNA sequences. Versions 9.42, 9.43 and subsequent releases of this dataset can be found in the "releases" directory. The most up-to-date version of the dataset can be found in the the "current" directory. Files in the "current" directory may contain additional improvements to the dataset that have not yet been incorporated into an official release.

We thank Margi Butler, Elena Casacuberta, Madeline Crosby, Bob Levis, Mary-Lou Pardue, Kevin O'Hare, Horacio Naveira, Dmitri Petrov, Steve Schaeffer, Todd Schlenke, Alfredo Villesante & the authors of REPBASE for sequences and/or annotations.