Introduction

Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic material from multiple individuals before high throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. We developed a novel method named TEMP, specifically designed to detect transposable element movements present with a wide range of frequencies in the population. By combining the information provided by pair-end reads and split reads, TEMP is able to identity both TE insertions and absences in genomic DNA sequences derived from heterogeneous samples, accurately estimate the frequencies of transposition events in the population, and pinpoint junctions of high frequency transposition events at single nucleotide resolution.

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Recent Updates

  • TEMP v1.01 Released May 28th 2014

    In this version we added a visualization feature that enables users to plot the distribution of TE polymorphisms across the genome easily. The newly added script will generate a JSON file from the TEMP output and then the users can load the JSON file into the web interface circosjs developed by Dr. Xiaopeng Zhu. Please read the TEMP manual for details.

Related Resources

Listed below are some useful resources related to TEMP. Some datasets contain a README file describing the detailed information about the dataset. Please read the README files carefully before using the files.

  • Download the supplementary material (including supplementary tables) of our NAR paper (3.02MB) here
  • Download the simulation datasets for evaluating TE discovery softwares (356.49GB) here
  • Download human test datasets (6.61GB) here
  • Download predicted transposition polymorphisms in Phase I DGRP lines (Dm6) (1.18MB) here

About us

TEMP is developed by Jiali Zhuang and Jie Wang in Dr. Zhiping Weng's lab at University of Massachusetts Medical School, Worcester, MA.
Visit our website to know more about who we are, our missions and our researches.
Please forward any questions about TEMP (or related resources), bug reports, suggestions and comments to Jiali Zhuang (jiali.zhuang@umassmed.edu)

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