We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices according to each case. We conclude with some future work directions and open problems. 1

We present the state of the art of the main component of text retrieval systems: the searching engine. We outline the main lines of research and issues involved. We survey recently published results for text searching and we explore the gap between theoretical vs. practical algorithms. The main observation is that simpler ideas are better in practice. 1597 Shaks. Lover's Compl. 2 From off a hill whose concaue wombe reworded A plaintfull story from a sistring vale. OED2, reword, sistering 1 1 Introduction Full text retrieval systems are becoming a popular way of providing support for on-line text. Their main advantage is that they avoid the complicated and expensive process of semantic indexing. From the end-user point of view, full text searching of on-line documents is appealing because a valid query is just any word or sentence of the document. However, when the desired answer cannot be obtained with a simple query, the user must perform his/her own semantic processing to guess w...

The problem of comparing two sequences A and B to determine their LCS or the edit distance between them has been much studied. In this paper we consider the following incremental version of these problems: given an appropriate encoding of a comparison between A and B, can one incrementally compute the answer for A and bB, and the answer for A and Bb with equal efficiency, where b is an additional symbol? Our main result is a theorem exposing a surprising relationship between the dynamic programming solutions for two such "adjacent" problems. Given a threshold k on the number of differences to be permitted in an alignment, the theorem leads directly to an O(k) algorithm for incrementally computing a new solution from an old one, as contrasts the O(k²) time required to compute a solution from scratch. We further show with a series of applications that this algorithm is indeed more powerful than its non-incremental counterpart by solving the applications with greater asymptotic ef...

The trend towards very large DNA sequencing projects, such as those being undertaken as part of the human genome initiative, necessitates the development of efficient and precise algorithms for assembling a long DNA sequence from the fragments obtained by shotgun sequencing or other methods. The sequence reconstruction problem that we take as our formulation of DNA sequence assembly is a variation of the shortest common superstring problem, complicated by the presence of sequencing errors and reverse complements of fragments. Since the simpler superstring problem is NP-hard, any efficient reconstruction procedure must resort to heuristics. In this paper, however, a four phase approach based on rigorous design criteria is presented, and has been found to be very accurate in practice. Our method is robust in the sense that it can accommodate high sequencing error rates and list a series of alternate solutions in the event that several appear equally good. Moreover it uses a limited form ...

The fragment assembly problem is that of reconstructing a DNA sequence from a collection of randomly sampled fragments. Traditionally the objective of this problem has been to produce the shortest string that contains all the fragments as substrings, but in the case of repetitive target sequences this objective produces answers that are overcompressed. In this paper, the problem is reformulated as one of finding a maximum-likelihood reconstruction with respect to the 2-sided Kolmogorov-Smirnov statistic, and it is argued that this is a better formulation of the problem. Next the fragment assembly problem is recast in graph-theoretic terms as one of finding a non-cyclic subgraph with certain properties and the objectives of being shortest or maximally-likely are also recast in this framework. Finally, a series of graph reduction transformations are given that dramatically reduce the size of the graph to be explored in practical instances of the problem. This reduction is ...

To date, most of the work on XML query and search has stemmed from the document management and database communities and from the information needs of business applications, as evidenced by existing XML query languages such as W3C's XQuery, which is strongly inspired by SQL. We propose here to extend the realm of XML by supporting the information needs of users wishing to query XML collections in a flexible way without knowing much about the documents structure. Rather than inventing a new query language, we suggest to query XML documents via pieces of XML documents or “XML fragments ” of the same nature as the documents that are queried. We then present an extension of the vector space model for searching XML collections and ranking search results by relevance 1

this paper, the text locations that are not filtered out are often referred to as surviving regions. Some filtering criteria are discussed in more detail in the next section

In this paper we study the problem of identifying meaningful patterns (i.e., motifs) from biological data. The general version of this problem is NP-hard. Numerous algorithms have been proposed in the literature to solve this problem. Many of these algorithms fall under the category of heuristics. We concentrate on exact algorithms in this paper. In particular, we concentrate on two different versions of the motif search problem and offer exact algorithms for them. 1

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This thesis focuses on the problem of text retrieval allowing errors, also called "approximate" string matching. The problem is to find a pattern in a text, where the pattern and the text may have "errors". This problem has received a lot of attention in recent years because of its applications in many areas, such as information retrieval, computational biology and signal processing, to name a few. The aim of this work is the development and analysis of novel algorithms to deal with the problem under various conditions, as well as a better understanding of the problem itself and its statistical behavior. Although our results are valid in many different areas, we focus our attention on typical text searching for information retrieval applications. This makes some ranges of values for the parameters of the problem more interesting than others. We have divided this presentation in two parts. The first one deals with on-line approximate string matching, i.e. when there is no time or space ...