A Dynamic Neighboring Extension Search Algorithm for Genome Coordinate Conversion in the Presence of Short Sequence Duplications

Oligonucleotide arrays are increasingly used in comparative genomic hybridization (CGH) to detect genomic copy number variation (CNV). The design of these arrays usually prefers uniquely mapped probes but routinely includes multiply mapped probes within a genome to maintain the high coverage and resolution. These duplicated probes could cause several limitations: besides their effects on the CNV calling, this kind of design also leads to the difficulty of converting genome coordinates between different genome assemblies. In this study, we tested over 385,000 probes for the genome coordinate conversion between two cattle genome assemblies and found out 33,910 (8.8%) of these probes cannot be uniquely mapped due to short sequence duplications. We also studied the distribution pattern of these short sequence duplications and discussed their potential impacts. Finally, we proposed and tested a dynamic neighboring extension search (DNES) algorithm to solve this conversion problem in order to facilitate a direct migration and comparison of array CGH results across different genome assemblies.