Approximate String Matching with Compressed Indexes
نویسندگان
چکیده
A compressed full-text self-index for a text T is a data structure requiring reduced space and able to search for patterns P in T . It can also reproduce any substring of T , thus actually replacing T . Despite the recent explosion of interest on compressed indexes, there has not been much progress on functionalities beyond the basic exact search. In this paper we focus on indexed approximate string matching (ASM), which is of great interest, say, in bioinformatics. We study ASM algorithms for Lempel-Ziv compressed indexes and for compressed suffix trees/arrays. Most compressed self-indexes belong to one of these classes. We start by adapting the classical method of partitioning into exact search to self-indexes, and optimize it over a representative of either class of self-index. Then, we show that a LempelZiv index can be seen as an extension of the classical q-samples index. We give new insights on this type of index, which can be of independent interest, and then apply them to a LempelZiv index. Finally, we improve hierarchical verification, a successful technique for sequential searching, so as to extend the matches of pattern pieces to the left or right. Most compressed suffix trees/arrays support the required bidirectionality, thus enabling the implementation of the improved technique. In turn, the improved verification largely reduces the accesses to the text, which are expensive in self-indexes. We show experimentally that our algorithms are competitive and provide useful space-time tradeoffs compared to classical indexes. Algorithms 2009, 2 1106
منابع مشابه
Indexed Hierarchical Approximate String Matching
We present a new search procedure for approximate string matching over suffix trees. We show that hierarchical verification, which is a well-established technique for on-line searching, can also be used with an indexed approach. For this, we need that the index supports bidirectionality, meaning that the search for a pattern can be updated by adding a letter at the right or at the left. This tu...
متن کاملApproximate String Matching with Lempel-Ziv Compressed Indexes
A compressed full-text self-index for a text T is a data structure requiring reduced space and able of searching for patterns P in T . Furthermore, the structure can reproduce any substring of T , thus it actually replaces T . Despite the explosion of interest on self-indexes in recent years, there has not been much progress on search functionalities beyond the basic exact search. In this paper...
متن کاملComputing Matching Statistics and Maximal Exact Matches on Compressed Full-Text Indexes
Exact string matching is a problem that computer programmers face on a regular basis, and full-text indexes like the suffix tree or the suffix array provide fast string search over large texts. In the last decade, research on compressed indexes has flourished because the main problem in large-scale applications is the space consumption of the index. Nowadays, the most successful compressed inde...
متن کاملFinding Approximate Matches in Large Lexicons
Approximate string matching is used for spelling correction and personal name matching. In this paper we show how to use string matching techniques in conjunction with lexicon indexes to find approximate matches in a large lexicon. We test several lexicon indexing techniques, including n-grams and permuted lexicons, and several string matching techniques, including string similarity measures an...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Algorithms
دوره 2 شماره
صفحات -
تاریخ انتشار 2009