Projects

Natural Transposable Element Project

Thank you for your interest in the natural transposable elements identified in the Drosophila melanogaster Release 3 euchromatic genomic sequence. We post updated versions of transposable element data as they become available while mantaining a repository of past versions at the bottom of this page. Each of these files has version numbers and dates and we strongly suggest that these be quoted whenever the data are used.

Natural Transposable Element Datasets Maintained by Michael Ashburner Last Updated: 8 April 2004

These files represent the set of natural transposable element sequences identified in D. melanogaster. These files are updated regularly by Michael Ashburner: ma11@gen.cam.ac.uk.
For details of versions please see: ASHBURNER_README

Natural Transposable Element Data Sets:
EMBL.FORMAT.v.9.4.1

FASTA.FORMAT.v.9.4.1

DMEL.TRANSPOSABLE.ELEMENTS.9.4.1.zip

Archived Data Sets:
DMEL.TRANSPOSABLE.ELEMENTS.9.2.zip

DMEL.TRANSPOSABLE.ELEMENTS.7.1.zip

DMEL.TRANSPOSABLE.ELEMENTS.6.2.zip

DMEL.TRANSPOSABLE.ELEMENTS.6.0.zip

DMEL.TRANSPOSABLE.ELEMENTS.5.01.zip

DMEL.TRANSPOSABLE.ELEMENTS.4.94.zip

DMEL.TRANSPOSABLE.ELEMENTS.4.92.zip


The following data were published in Genome Biology, and have been archived below as frozen data sets.
Any questions should be directed to Josh Kaminker: joshk@fruitfly.org

Natural Transposable Element Datasets as Described in Kaminker et al. Last Updated: 25 October 2003

Each sequence in fastA format is flanked by 500bp of unique sequence and is identified with a descriptive header containing a unique FBti identifier. For nested elements, each nest has a unique FBti identifier as do the component elements. Individual nested elements are represented in all datasets below, while the complete nest is only represented in the Nested Transposable Element dataset. As some of these files are rather large, we suggest that you use the SAVE AS option in your browser when viewing these data.
For details of versions please see: KAMINKER_README


Canonical Sequences Transposable Element Sequences Used in Distance Calculations Transposable Element Sequences NOT Used in Distance Calculations All Transposable Element Sequences Identified in Analysis
FASTA.v2 EMBL.v2 CANONICAL.v1.zip FB.FASTA.v3 LTR.FASTA.v3 LINE.FASTA.v3 TIR.FASTA.v3 FASTA.v3 (ALL FAMILIES) GFF.v3 (ALL FAMILIES) LTR.FASTA.v3 LINE.FASTA.v3 TIR.FASTA.v3 FB.FASTA.v3 FASTA.v3 (ALL FAMILIES) GFF.v3 (ALL FAMILIES) LTR.FASTA.v3 LINE.FASTA.v3 TIR.FASTA.v3 FB.FASTA.v3 FASTA.v3 (ALL FAMILIES) GFF.v3 (ALL FAMILIES)

Alignments in MASE Format: (These can be viewed using the SeaView program)
MASE.ALIGNMENTS.v3.ZIP

Nested Transposable Elements: (File includes complete nests as well as component elements)
NESTED.TRANSPOSONS.FASTA.v3

Archived Transposable Element Datasets:
TRANSPOSABLEELEMENTS.V1.ZIP

TRANSPOSABLEELEMENTS.V2.ZIP