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Yilan Liu
The next-generation sequencing technologies are pouring big data and pushing the frontier of life sciences toward new territories that were never imagined before. However, such big data impose great computational challenges to statistical analysis of these data. It is important to utilize Graphics Processing Unit (GPU)’s large throughput and massive parallelism to process large data […]
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Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng
BLAST, short for Basic Local Alignment Search Tool, is a fundamental algorithm in the life sciences that compares biological sequences. However, with the advent of next-generation sequencing (NGS) and increase in sequence read-lengths, whether at the outset or downstream from NGS, the exponential growth of sequence databases is arguably outstripping our ability to analyze the […]
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Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, […]
Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi
MOTIVATION AND OBJECTIVES: In genotyping analysis often researchers need to merge together genetic datasets coming from different genotyping platforms that use different sets of Single Nucleotide Polymorphisms (SNPs) to represent genetic polymorphisms. In order to do this, it is necessary to know the exact position of a SNP in a chromosome and update this information […]
Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama
BACKGROUND: A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, […]
Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann
MOTIVATION: The introduction of next-generation sequencing techniques and especially the high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of short reads to reference sequences a standard application in modern bioinformatics. Short-read alignment is needed for reference based re-sequencing of complete genomes as well as for gene expression analysis based on transcriptome sequencing. […]
Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann
MOTIVATION: The introduction of next generation sequencing techniques and especially the high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of short reads to reference sequences a standard application in modern bioinformatics. Short read alignment is needed for reference based re-sequencing of complete genomes as well as for gene expression analysis based on […]
Yongchao Liu, Bertil Schmidt, Douglas Maskell
BACKGROUND: Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the de novo assembly in terms of assembly quality and scalability for large-scale short read datasets. RESULTS: We present […]
Ashwin M. Aji, Liqing Zhang, Wu C. Feng
Next-generation, high-throughput sequencers are now capable of producing hundreds of billions of short sequences (reads) in a single day. The task of accurately mapping the reads back to a reference genome is of particular importance because it is used in several other biological applications, e.g., genome re-sequencing, DNA methylation, and ChiP sequencing. On a personal […]
John L. Van Hemert, Julie A. Dickerson
Statistical tests are often performed to discover which experimental variables are reacting to specific treatments. Time-series statistical models usually require the researcher to make assumptions with respect to the distribution of measured responses which may not hold. Randomization tests can be applied to data in order to generate null distributions non-parametrically. However, large numbers of […]

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