Mar 27, 2015

Index-based map-to-sequence alignment in large eukaryotic genomes

BioRxiv : the Preprint Server for Biology
Davide VerzottoNiranjan Nagarajan

Abstract

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and mapping technologies (e.g. optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kbp–2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging due to the lack of efficient and freely available software for robustly aligning maps to sequences. Here we introduce two new map-to-sequence alignment algorithms that efficiently and accurately align high-throughput mapping datasets to large, eukaryotic genomes while accounting for high error rates. In order to do so, these methods (OPTIMA for glocal and OPTIMA-Overlap for overlap alignment) exploit the ability to create efficient data structures that index continuous-valued mapping data while accounting for errors. We also introduce an approach for evaluating the significance of alignments that avoids expensive permutation-based tests while being agnostic to technology-dependent err...Continue Reading

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Mentioned in this Paper

Computer Software
Laboratory Procedures
Genome
High Throughput Technology
Evaluation
Sequencing
Structure
probe gene fragment
Optical Restriction Mapping
Mapping, Vessel

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