chainCleaner

chainCleaner refines genome alignments by detecting and removing misleading local alignments to improve specificity and recover fragmented orthologous exon alignments for comparative analyses of human and other vertebrate genomes.

Key Features:

• Improved Specificity: Detects and removes local alignments, including those arising from pseudogenes, that can confound true evolutionary relationships.
• Revealing Hidden Alignments: Exposes alignments between exons of orthologous genes that were previously obscured by misleading local alignments.
• Enhanced Sensitivity: Recovers alignment regions that would otherwise fall below a minimum score threshold due to fragmentation, increasing overall alignment sensitivity.
• Fast Systematic Testing: Applies a fast computational approach that systematically tests alignments with emphasis on human and other vertebrate genomes.

Scientific Applications:

• Comparative Genomics: Produces more accurate genome alignments for analyses of evolutionary relationships and gene conservation between humans and other vertebrates.
• Genomic Rearrangement Studies: Detects and corrects misalignments caused by genomic rearrangements to clarify complex evolutionary events across species.

Methodology:

chainCleaner employs a fast computational approach that systematically tests alignments, particularly between human and other vertebrate genomes, by identifying local alignments that may obscure true evolutionary signals and removing those misleading alignments.