Hardware Accelerated Sequence Alignment with Traceback

نویسندگان
چکیده

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Hardware Accelerated Sequence Alignment with Traceback

Recommended by Cesar Torres Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequenc...

متن کامل

Hardware accelerator architecture for simultaneous short-read DNA sequences alignment with enhanced traceback phase

Dynamic programming algorithms are widely used to find the optimal sequence alignment between any two DNA sequences. This manuscript presents a new, flexible and scalable hardware accelerator architecture to speedup the implementation of the frequently used Smith–Waterman algorithm. When integrated with a general purpose processor, the developed accelerator significantly reduces the computation...

متن کامل

CAFE: aCcelerated Alignment-FrEe sequence analysis

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software,...

متن کامل

Parallel hardware for sequence comparison and alignment

Sequence comparison, a vital research tool in computational biology, is based on a simple O(n2) algorithm that easily maps to a linear array of processors. This paper reviews and compares high-performance sequence analysis on general-purpose supercomputers and single-purpose reconfigurable, and programmable co-processors. The difficulty of comparing hardware from published performance figures i...

متن کامل

Hardware Acceleration of Genetic Sequence Alignment

Next generation DNA sequencing machines have been improving at an exceptional rate; the subsequent analysis of the generated sequenced data has become a bottleneck in current systems. This paper explores the use of reconfigurable hardware to accelerate the short read mapping problem, where the positions of millions of short DNA sequences are located relative to a known reference sequence. The p...

متن کامل

ذخیره 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: International Journal of Reconfigurable Computing

سال: 2009

ISSN: 1687-7195,1687-7209

DOI: 10.1155/2009/762362