Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
نویسندگان
چکیده
منابع مشابه
Exact and complete short read alignment to microbial genomes using GPU programming
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 transcr...
متن کاملShort read alignment with populations of genomes
SUMMARY The increasing availability of high-throughput sequencing technologies has led to thousands of human genomes having been sequenced in the past years. Efforts such as the 1000 Genomes Project further add to the availability of human genome variation data. However, to date, there is no method that can map reads of a newly sequenced human genome to a large collection of genomes. Instead, m...
متن کاملOnline Image Classification Using Graphics Processing Unit- Based Genetic Programming
A texture classification vision system implemented with Graphics Processing Unit-based genetic programming is described. An online learning environment is implemented, in which genetic programming is automatically invoked when unclassified texture instances are present in an image stream. Once a segment is positively classified, the genetic programming classifier expression is reapplied to fram...
متن کاملImprovement and parallelization of Snort network intrusion detection mechanism using graphics processing unit
Nowadays, Network Intrusion Detection Systems (NIDS) are widely used to provide full security on computer networks. IDS are categorized into two primary types, including signature-based systems and anomaly-based systems. The former is more commonly used than the latter due to its lower error rate. The core of a signature-based IDS is the pattern matching. This process is inherently a computatio...
متن کاملSolving Quadratic Programming Problems on Graphics Processing Unit
Quadratic Programming (QP) problems frequently appear as core component when solving constrained optimal control or estimation problems. The focus of this paper is on accelerating an existing Interior Point Method (IPM) for solving QP problems by exploiting the parallel computing characteristics of GPU. We compare the so-called data-parallel and the problem-parallel approaches to achieve speed ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2011
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btr151