Index of /12_species_analysis/genomes/aaa/transposable_elements/caspi

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[ ]DroAna.gff3.gz 2006-12-22 18:07 305K 
[ ]DroCAF1gff3.tar.bz2 2006-12-22 18:32 3.2M 
[ ]DroEre.gff3.gz 2006-12-22 18:07 224K 
[ ]DroGri.gff3.gz 2006-12-22 18:19 340K 
[ ]DroMel.gff3.gz 2006-12-22 18:07 218K 
[ ]DroMoj.gff3.gz 2006-12-22 18:07 406K 
[ ]DroPer.gff3.gz 2006-12-22 18:16 344K 
[ ]DroPse.gff3.gz 2006-12-22 18:27 317K 
[ ]DroSec.gff3.gz 2006-12-22 18:21 206K 
[ ]DroSim.gff3.gz 2006-12-22 18:08 234K 
[ ]DroVir.gff3.gz 2006-12-22 18:08 373K 
[ ]DroWil.gff3.gz 2006-12-22 18:08 609K 
[ ]DroYak.gff3.gz 2006-12-22 18:08 228K 
Data for CAF1 12 Drosophila Genome Assemblies

Data

 

Transposable element annotations for twelve drophila genomes, CAF1 assembly

E-mail:email

Fax: 510-642-8204

Description: This document contains annotations for repeat elements in twelve drosophila genomes (CAF1 assemblies). The regions are highly enriched for transposable elements. The files can be loaded into the UCSC browser for viewing. Where available, the annotations also contain information about the branch on which the insertion is likely to have occured. When the branch information lists only one genome, it is presumed that the insertion occured on the terminal branch after that genome's speciation from its closest sister taxa of the twelve. When the branch information lists a number of genomes, it is presumed that the insertion occured on the branch before the closest common ancestor before the genomes in the list. These annotations do not contain family associations. When using these data, please cite the methods paper:

Caspi, A. and Pachter, L. (2006). ''Identification of transposable elements using multiple alignments of related genomes.'' Genome Research 16:260-270.

 

 


The data is in GFF3 format, browsable by the UCSC genome browser:

Table 1, D.melanogaster TE annotations (CAF1 assembly).

Table 2, D.simulans TE annotations (CAF1 assembly).

Table 3, D.sechelia TE annotations (CAF1 assembly).

Table 4, D.erecta TE annotations (CAF1 assembly).

Table 5, D.yakuba TE annotations (CAF1 assembly).

Table 6, D.pseudoobscura TE annotations (CAF1 assembly).

Table 7, D.persimilis TE annotations (CAF1 assembly).

Table 8, D.mojavensis TE annotations (CAF1 assembly).

Table 9, D.grimshawi TE annotations (CAF1 assembly).

Table 10, D.virilis TE annotations (CAF1 assembly).

Table 11, D.wilistoni TE annotations (CAF1 assembly).

Table 12, D.ananasae TE annotations (CAF1 assembly).

Table 13, All 12 genome TE annotations (CAF1 assembly) in tar/bzip2.