PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Identifying dispersed repeats is crucial for genome annotation.
• Existing tools often produce fragmented results due to sequence divergence.
• Merging these fragments is challenging, especially for large or mutated elements.

Purpose of the Study:

• To develop a post-processing tool for merging fragmented repeat sequences.
• To improve the accuracy of identifying ancient mobile genetic elements.
• To provide a visual inspection method for repeat identification results.

Main Methods:

• Developed PLOTREP, a software tool for post-processing sequence similarity search results.
• Implemented a method to merge sequence fragments belonging to the same repeat copy.
• Integrated a dot-plot like graphical output for visual inspection.

Main Results:

• PLOTREP effectively merges fragmented repeat sequences.
• The tool aids in identifying complete ancient mobile element copies.
• Provides rapid visual inspection of repeat identification results.

Conclusions:

• PLOTREP enhances genome annotation by improving repeat identification accuracy.
• The tool addresses the challenge of fragmented repeat data.
• Offers a user-friendly web implementation for broader accessibility.