Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

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

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become more complex everyday, requiring fast queries to multiple genomes. In this ...

متن کامل

A New Parallel Partition Algorithm for Parallel Suffix Tree Construction

The suffix tree is a compacted trie of all suffixes of a given string. It is a fundamental data structure in a wide range of domains such as text processing, data compression, computer vision, computational biology, and so on [1]. Moreover, it can be used for network researches such as web analysis, which has been studied actively [2], [3]. For example, suffix trees have been utilized to effect...

متن کامل

Scalable Parallel Suffix Array Construction

Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. We describe the first implementation and experimental evaluation of a scalable parallel algorithm for suffix array construction. The implementation works on distributed memory computers using MPI, Experi...

متن کامل

A Simple Parallel Cartesian Tree Algorithm and its Application to Suffix Tree Construction

We present a simple linear work and space, and polylogarithmic time parallel algorithm for generating multiway Cartesian trees. As a special case, the algorithm can be used to generate suffix trees from suffix arrays on arbitrary alphabets in the same bounds. In conjunction with parallel suffix array algorithms, such as the skew algorithm, this gives a rather simple linear work parallel algorit...

متن کامل

Parallel Suffix Array Construction by Accelerated Sampling

A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique that we call accelerated sampling. It runs in optimal O( p ) local computation and communication, and requires a near optimal O(log log p) supersteps. The algorithm provides an improvement over the synchronisation costs of existing algorithms, and reinforces the importance of the...

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: Journal of Computational Biology

سال: 2014

ISSN: 1066-5277,1557-8666

DOI: 10.1089/cmb.2012.0256