Finding approximate overlaps is the first phase of many sequence assembly methods. Given a set of r strings of total length n and an error-rate , the goal is to find, for all-pairs of strings, their suffix/prefix matches (overlaps) that are within edit distance k = d `e, where ` is the length of the overlap. We propose new solutions for this problem based on backward backtracking (Lam et al. 20...

Current concatenative morphological analyzers consider prefix, suffix and stem morphemes based on lexicons of morphemes, and morpheme concatenation rules that determine whether prefix-stem, stem-suffix, and prefix-suffix concatenations are allowed. Existing affix lexicons contain extensive redundancy, suffer from inconsistencies, and require significant manual work to augment with clitics and p...

We consider the problem of retrieving multiple documents relevant to the single subtopics of a given web query, termed “full-subtopic retrieval”. To solve this problem we present a novel search results clustering algorithm that generates clusters labeled by keyphrases. The keyphrases are extracted from the generalized suffix tree built from the search results and merged through an improved hier...

The time complexity of suffix tree construction has been shown to be equivalent to that of sorting: O(n) for a constant-size alphabet or an integer alphabet and O(n logn) for a general alphabet. However, previous algorithms for constructing suffix arrays have the time complexity of O(n logn) even for a constant-size alphabet. In this paper we present a linear-time algorithm to construct suffix ...

Phrase has been considered as a more informative feature term for improving the effectiveness of document retrieval .This paper propose an Algorithm A Phrase Based Document Retrieval to retrieve the similar documents by combining two exiting algorithm suffix tree ,index data structure and “The Boyer-Moore Algorithm”, faster string searching algorithm. The suffix tree is constructed based on E. ...

MOTIVATION A central problem in genomics is to determine the function of a protein using the information contained in its amino acid sequence. Variable length Markov chains (VLMC) are a promising class of models that can effectively classify proteins into families and they can be estimated in linear time and space. RESULTS We introduce a new algorithm, called Sparse Probabilistic Suffix Trees...