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 |
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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. |
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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have been archived below as frozen data sets.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
- The transposable
elements of Drosophila melanogaster - a genomics
perspective
Joshua S. Kaminker, Casey M. Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A. Wheeler, Suzanna Lewis, Gerald M. Rubin, Michael Ashburner and Susan E. Celniker
Genome Biology (2002) 3:research0084.1-0084.20
| Natural Transposable Element Datasets as Described in Kaminker et al. | Last Updated: 25 October 2003 |
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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. |
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| Canonical Sequences | Transposable Element Sequences Used in Distance Calculations | Transposable Element Sequences NOT Used in Distance Calculations | All Transposable Element Sequences Identified in Analysis |
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| 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