Please use this identifier to cite or link to this item:
|Title:||A space and time efficient algorithm for constructing compressed suffix arrays|
|Source:||Hon, W.-K., Lam, T.-W., Sadakane, K., Sung, W.-K., Yiu, S.-M. (2007). A space and time efficient algorithm for constructing compressed suffix arrays. Algorithmica (New York) 48 (1) : 23-36. ScholarBank@NUS Repository. https://doi.org/10.1007/s00453-006-1228-8|
|Abstract:||With the first human DNA being decoded into a sequence of about 2.8 billion characters, much biological research has been centered on analyzing this sequence. Theoretically speaking, it is now feasible to accommodate an index for human DNA in the main memory so that any pattern can be located efficiently. This is due to the recent breakthrough on compressed suffix arrays, which reduces the space requirement from O(n log n) bits to O(n) bits. However, constructing compressed suffix arrays is still not an easy task because we still have to compute suffix arrays first and need a working memory of O(n log n) bits (i.e., more than 13 gigabytes for human DNA). This paper initiates the study of constructing compressed suffix arrays directly from the text. The main contribution is a construction algorithm that uses only O(n) bits of working memory, and the time complexity is O(n log n). Our construction algorithm is also time and space efficient for texts with large alphabets such as Chinese or Japanese. Precisely, when the alphabet size is |∑|, the working space is O(n log |∑|) bits, and the time complexity remains O(n log n), which is independent of |∑|. © Springer 2007.|
|Source Title:||Algorithmica (New York)|
|Appears in Collections:||Staff Publications|
Show full item record
Files in This Item:
There are no files associated with this item.
checked on Jan 16, 2018
WEB OF SCIENCETM
checked on Dec 13, 2017
checked on Jan 21, 2018
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.