PlotRep

PlotRep merges fragmented sequence similarity search hits to reconstruct dispersed repeat copies and produce coherent representations of ancient mobile elements for genome annotation and evolutionary analysis.

Key Features:

• Fragment Merging: Merges fragments that belong to the same copy of dispersed repeats, accommodating nucleotide substitutions, deletions, and insertions.
• Post-Processing Capability: Post-processes sequence similarity search results against precompiled repeat reference libraries to integrate fragments into coherent repeat copies despite evolutionary divergence.
• Visual Inspection: Generates dot-plot-like graphical outputs to visualize relationships and alignments between genomic sequences and repeat libraries.

Scientific Applications:

• Genome annotation: Improves identification and completeness of dispersed repeats in genome annotation projects by merging fragmented sequences.
• Reconstruction of ancient mobile elements: Enables reconstruction of ancient copies of mobile elements from fragmented, diverged sequences.
• Evolutionary and functional analysis: Facilitates studies of genomic evolution and the functional roles of mobile elements by recovering degraded repeat copies.

Methodology:

Processes sequence similarity search results from precompiled repeat reference libraries, analyzes hits with sensitivity to nucleotide substitutions, deletions, and insertions, and identifies and merges related fragments into coherent repeat copies.