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

Permanent URL:
http://handle.nal.usda.gov/10113/42509
Abstract:
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.
Author(s):
Zhu, Bin , Jiang, Lu , Liu, George E.
Subject(s):
cattle , genome , animal genetics , genetic techniques and protocols , nucleic acid hybridization , DNA probes , repetitive sequences , physical chromosome mapping , algorithms , bioinformatics
Format:
p. 29-36.
Note:
Includes references
Source:
Gene Expression to Genetical Genomics 2009, v. 2
Language:
English
Year:
2009
Collection:
Journal Articles, USDA Authors, Peer-Reviewed
File:
Download [PDF File]
Rights:
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.