RepeatFiller

RepeatFiller enhances genome alignments by incorporating previously undetected local alignments between repetitive sequences, including transposable elements.

Key Features:

• Incorporation of repeat-overlapping alignments: Integrates newly detected repeat-overlapping local alignments into existing pairwise alignment chains by focusing on regions bounded by colinear aligning blocks.
• Efficient handling of repetitive sequences: Targets repeat-overlapping seeds within those local regions to avoid the prohibitive computational cost of considering all seeds genome-wide and to overcome limitations of seed-and-extend heuristics.
• Improved genome alignment coverage: Recovered between 22 and 84 Mb of previously undetected alignments in human versus 20 other representative mammals, predominantly overlapping transposable elements.
• Enhanced annotation of conserved non-exonic elements: Identifies novel transposon-derived elements evolving under constraint and removes thousands of elements not conserved in placental mammals, refining conserved non-exonic element annotation.

Scientific Applications:

• Genome evolution analyses: Enables recovery of repeat-overlapping alignments across species to study evolutionary changes in repetitive DNA.
• Transposable element co-option studies: Facilitates investigation into the functional co-option of transposable elements and their contributions to evolutionary novelty and adaptability.
• Conserved non-coding element curation: Improves identification and refinement of conserved non-exonic (non-coding) elements and their roles in genome regulation.

Methodology:

Refines existing pairwise alignment chains by adding repeat-overlapping local alignments within regions defined by colinear aligning blocks, thereby considering seeds that overlap repeats while limiting computational cost.