PicoInversionMiner

PicoInversionMiner detects pico-inplace-inversions by re-analyzing genomic alignment data to identify minute in-place inversions between closely related species for comparative and evolutionary analyses.

Key Features:

• Detection of pico-inplace-inversions: Identifies small inplace-inversions that are often missed by standard genomic aligners.
• Likelihood ratio test: Uses a likelihood ratio test to screen alignment data for statistical evidence of pico-inplace-inversions.
• Re-analysis of existing alignments: Re-analyzes alignment data from resources such as the UCSC Genome Browser to locate candidate inversions.
• Targeting micro- and pico-inplace-inversions: Specifically targets micro-inplace-inversions and pico-inplace-inversions within alignment datasets.

Scientific Applications:

• Comparative genomics: Detects fine-scale inversion differences between closely related species, including human and chimpanzee genomes.
• Genomic architecture and evolution: Reveals additional in-place inversions to improve understanding of genomic architecture and evolutionary processes.

Methodology:

It re-analyzes alignment data (e.g., UCSC Genome Browser), targets micro- and pico-inplace-inversions, and screens candidate regions using a likelihood ratio test.