A quick tour on suffix arrays and compressed suffix arrays
نویسندگان
چکیده
منابع مشابه
Compressed Spaced Suffix Arrays
Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data structure, either a hash table or a spaced suffix array (SSA). In this paper we show how to compress SSAs relative to normal suffix arrays (SAs) and still su...
متن کاملA Simple Introduction to Compressed Suffix Arrays
This document attempts to provide a simple introduction to a quite fun, and possibly-becominguseful full-text index structure: The compressed suffix array. I have tried to write this document so that it’s accessible to a reader with a comfortable grasp of advanced undergraduate computer science concepts in both theory and systems. Please let me know if that’s not the case.
متن کاملSuffix Trees and Suffix Arrays
Iowa State University 1.1 Basic Definitions and Properties . . . . . . . . . . . . . . . . . . . . 1-1 1.2 Linear Time Construction Algorithms . . . . . . . . . . . . . 1-4 Suffix Trees vs. Suffix Arrays • Linear Time Construction of Suffix Trees • Linear Time Construction of Suffix Arrays • Space Issues 1.3 Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...
متن کاملCompressed Suffix Arrays for Massive Data
We present a fast space-efficient algorithm for constructing compressed suffix arrays (CSA). The algorithm requires O(n logn) time in the worst case, and only O(n) bits of extra space in addition to the CSA. As the basic step, we describe an algorithm for merging two CSAs. We show that the construction algorithm can be parallelized in a symmetric multiprocessor system, and discuss the possibili...
متن کاملSuffix Arrays on Words
Surprisingly enough, it is not yet known how to build directly a suffix array that indexes just the k positions at word-boundaries of a text T [1, n], taking O(n) time and O(k) space in addition to T . We propose a class-note solution to this problem that achieves such optimal time and space bounds. Word-based versions of indexes achieving the same time/space bounds were already known for suffi...
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: Theoretical Computer Science
سال: 2011
ISSN: 0304-3975
DOI: 10.1016/j.tcs.2010.12.036