SUMMARY: Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These methods often depend on the wealth of information already collected. The explosion in the number of newly available sequences calls for novel methods to explore local sequence similarity. We have developed a new method for iterative motif scanning that will look for ungapped sequence patterns similar to a submitted query. Using careful parameter estimation and an adaptation of a fast string-matching algorithm, the method performs significantly better in this context than the existing software. AVAILABILITY AND IMPLEMENTATION: The IGLOSS web server is available at http://compbioserv.math.hr/igloss/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Summary Finite‐state automata are important components in information retrieval and natural language processing software. A recursive automaton is the most compact representation of the acyclic deterministic finite‐state automata. It is based on merging not only the equivalent states but also the identical substructures in an automaton. The LZ trie variant is the state‐of‐the‐art in automata compression regarding space, but the time needed for its construction was, until now, quadratic, which has made it impractical for large inputs. In this paper, we present the first algorithm for LZ trie construction that runs in effectively linear time thereby making it an attractive choice for finite‐state automata implementation. We achieve this goal by adding a new functionality to the enhanced suffix array data structure. We present two variants of the construction procedure – an optimal method regarding the final size and a method that sacrifices some compression for low intermediate memory usage. We have made the implementation of our algorithms available in an open source software package LzLex.Copyright © 2014 John Wiley & Sons, Ltd.

An efficient algorithm for trie compression has already been described. Here we present its practical value and demonstrate its superiority in terms of space savings to other methods of lexicon compression. Apart from simple lexicons, a compressed trie can, with some additional processing, be used as a component in the compact representation of simple static databases. We present the potential of the algorithm in compressing natural language dictionaries. Copyright © 2005 John Wiley & Sons, Ltd.

Summary form only given. Lexicon lookup is an essential part of almost every natural language processing system. A natural language lexicon is a set of strings where each string consists of a word and the associated linguistic data. Its computer representation is a structure that returns appropriate linguistic data on a given input word. It should be small and fast. We propose a method for lexicon compression based on a very efficient trie compression method and the inverted file paradigm. The method was applied on a 664000 string, 18 Mbyte, French phonetic and grammatical electronic dictionary for spelling-to-phonetics conversion. Entries in the lexicon are strings consisting of a word, its phonetic transcription, and some additional codes.