Scalable parallel suffix array construction
نویسندگان
چکیده
منابع مشابه
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...
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A suffix array represents the suffixes of a string in sorted order. Being a simpler and more compact alternative to suffix trees, it is an important tool for full text indexing and other string processing tasks. We introduce the skew algorithm for suffix array construction over integer alphabets that can be implemented to run in linear time using integer sorting as its only nontrivial subroutin...
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We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA ...
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ژورنال
عنوان ژورنال: Parallel Computing
سال: 2007
ISSN: 0167-8191
DOI: 10.1016/j.parco.2007.06.004