FlyTE: Transposable element discovery, annotation and population frequency in flies

Wesley fleming art sculpture

From individuals to population
Stanford University


  This database contains annotation and calls of Transposable element (TE) insertions in Drosophila melanogaster. The database already stores several millions entries (TE calls). The database allows you to obtain annotation and frequency of individual TE insertions in specific populations.


  Methods
  T-lex2 is the most complete computational package available to date for the discovery, annotation and reannotation, and population genetic analysis of TEs ( Fiston-Lavier et al. 2011). T-lex2 was used to re-annotate 10% of the TE insertions annotated in the reference D. melanogaster genome. We are now using T-lex2 to discover and annotate the TE insertions in multiple D. melanogaster populations. Experimental or additonal computational approaches are taken into account to provide the most accurate annotation and frequency estimation currently possible.


  Populations
   More than 300 strains
collected from around the world have been completely sequenced. Their genomic sequences are provided by two main sequencing projects called DGRP (Drosophila Genome Reference Panel) and DPGP2 (Drosophila Population Genome Project 2).

  In the summary table below, you will find more info about the population data available today. For each population, the TE insertions specifically discovered in the population but absent from the reference sequence (see column 'population-specific TEs') and the presence/absence calls of all TE insertions (i.e., reference and population-specific) are also provided (see column 'TE calls'). The pre-computed TE frequency for all the TE insertions are provided as well (see the column 'TE freq.').


   PopDrowser: the Population Drosophila Browser. Ramia M, Librado P, Casillas S, Rozas J and Barbadilla A. Bioinformatics (2012) 28 (4): 595-596. doi: 10.1093/bioinformatics/btr691.

   T-lex2: a package for the discovery, annotation, re-annotation and population frequency estimate of transposable element using next-generation sequencing data. Fiston-Lavier AS, Barron M, Gonzalez J and Petrov DA. (in prep)

   T-lex: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Fiston-Lavier AS, Carrigan M, Petrov DA and Gonzalez J. Nuc. Acids. Res. 2011 Mar 1;39(6):e36.


   FlyTE: Transposable element discovery, annotation and population frequency in flies. Fiston-Lavier AS, Barrientos M, Ramia M, Barron M, Tushar D, Barbadilla A and Petrov DA. (in prep)