AGE

The software tool "AGE" addresses the problem of defining the precise location of structural variations (SVs) at single-nucleotide breakpoint resolution, which is necessary for classifying SVs, evaluating their functional impact, and reconstructing personal genome sequences. It uses a dynamic-programming algorithm called Alignment with Gap Excision (AGE) that simultaneously aligns the 5' and 3' ends of two given sequences and introduces a 'large-gap jump' between the local end alignments to maximize the total alignment score. AGE can be extended to tandem duplications, inversions, and complex events involving two large gaps. AGE was applied for breakpoint determination and standardization in the 1000 Genomes Project by aligning locally assembled contigs to the human genome.