DNA

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations

Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly …

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

MOTIVATION: The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely …

Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing

The pyrosequencing technology from 454 Life Sciences and a novel assembly approach for cDNA sequences with the Newbler Assembler were used to achieve a major step forward to unravel the transcriptome of Chinese hamster ovary (CHO) cells. Normalized …

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

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. …