ADaM: augmenting existing approximate fast matching algorithms with efficient and exact range queries

BMC Bioinformatics

Research

Lee P Thompson¹  Nathan L Clement¹  Daniel P Miranker¹ 

[1] Department of Computer Science, University of Texas at Austin, 2317 Speedway, Stop D9500, 78712, Austin, TX, USA;

关键词: Distance Function;    Range Query;    Query Point;    Mapping Accuracy;    Query Time;   

DOI  :  10.1186/1471-2105-15-S7-S1

来源: Springer

【 摘 要 】

BackgroundDrug discovery, disease detection, and personalized medicine are fast-growing areas of genomic research. With the advancement of next-generation sequencing techniques, researchers can obtain an abundance of data for many different biological assays in a short period of time. When this data is error-free, the result is a high-quality base-pair resolution picture of the genome. However, when the data is lossy the heuristic algorithms currently used when aligning next-generation sequences causes the corresponding accuracy to drop.ResultsThis paper describes a program, ADaM (A PF D NA M apper) which significantly increases final alignment accuracy. ADaM works by first using an existing program to align "easy" sequences, and then using an algorithm with accuracy guarantees (the APF) to align the remaining sequences. The final result is a technique that increases the mapping accuracy from only 60% to over 90% for harder-to-align sequences.

【 授权许可】

CC BY   
© Clement et al.; licensee BioMed Central Ltd. 2014