Reducing the space requirement of suffix trees

نویسنده

  • Stefan Kurtz
چکیده

We show that suffix trees store various kinds of redundant information. We exploit these redundancies to obtain more space efficient representations. The most space efficient of our representations requires 20 bytes per input character in the worst case, and 10.1 bytes per input character on average for a collection of 42 files of different type. This is an advantage of more than 8 bytes per input character over previous work. Our representations can be constructed without extra space, and as fast as previous representations. The asymptotic running times of suffix tree applications are retained. Copyright  1999 John Wiley & Sons, Ltd.

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Suffix Vector: Space- and Time-Efficient Alternative to Suffix Trees

Suffix trees are versatile data structures that are used for solving many string-matching problems. One of the main arguments against widespread usage of the structure is its space requirement. This paper describes a new structure called suffix vector, which is not only better in terms of storage space but also simpler than the most efficient suffix tree representation known to date. Alternativ...

متن کامل

The Virtual Suffix Tree: An Efficient Data Structure for Suffix Trees and Suffix Arrays

We introduce the VST (virtual suffix tree), an efficient data structure for suffix trees and suffix arrays. Starting from the suffix array, we construct the suffix tree, from which we derive the virtual suffix tree. The VST provides the same functionality as the suffix tree, including suffix links, but at a much smaller space requirement. It has the same linear time construction even for large ...

متن کامل

Relative Suffix Trees

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while us...

متن کامل

Compact Suffix Trees Resemble PATRICIA Tries: Limiting Distribution of the Depth

Suffix trees are the most frequently used data structures in algorithms on words. In this paper, we consider the depth of a compact suffix tree, also known as the PAT tree, under some simple probabilistic assumptions. For a biased memoryless source, we prove that the limiting distribution for the depth in a PAT tree is the same as the limiting distribution for the depth in a PATRICIA trie, even...

متن کامل

An empirical evaluation of a metric index for approximate string matching

In this paper, we evaluate a metric index for the approximate string matching problem based on suffix trees, proposed by Gonzalo Navarro and Edgar Chávez [9]. Suffix trees are used during the index construction to generate intermediate data (pivot table) that to be indexed and the query processing. One of the main problems with suffix trees is their space requirements. To address this, we propo...

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

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Softw., Pract. Exper.

دوره 29  شماره 

صفحات  -

تاریخ انتشار 1999