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RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation
1Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria.
Bioinformatics (Oxford, England)
|August 31, 2018
Summary
RepeatCraft is a new pipeline that reconstructs fragmented repetitive elements in genomes. This improves the classification and evolutionary analysis of these important genomic components.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Repetitive elements constitute a significant portion of many genomes, influencing genome evolution and gene regulation.
- Accurate classification and evolutionary analysis of repetitive elements are crucial but hindered by fragmented repeat loci.
- Existing tools often produce fragmented results, complicating the study of novel repeats and their evolutionary history.
Purpose of the Study:
- To develop an integrated pipeline, RepeatCraft, for improved classification and analysis of repetitive elements in genomes.
- To address the challenge of fragmented repeat loci by reconstructing longer, contiguous copies.
- To facilitate better annotation and sequence comparisons of repetitive elements.
Main Methods:
- RepeatCraft integrates results from multiple repeat element classification tools.
- The pipeline utilizes both sequence similarity and structural features for classification.
- It employs a de-fragmentation process to reconstruct contiguous repeat loci.
- A user-friendly web-based interface allows for data exploration.
Main Results:
- RepeatCraft successfully de-fragments closely spaced repeat loci, reconstructing longer repeat copies.
- The pipeline enables more accurate annotation and facilitates sequence comparisons of repetitive elements.
- Improved reconstruction of repeat loci enhances the classification of novel repeats and their evolutionary analyses.
Conclusions:
- RepeatCraft offers a robust solution for overcoming the fragmentation issue in repetitive element analysis.
- The pipeline enhances the study of genome evolution and regulation by providing better insights into repetitive elements.
- RepeatCraft provides an accessible platform for researchers to explore and analyze repeat data.
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