The suffix tree of alignment is an index data structure for similar strings. Given an alignment of similar strings, it stores all suffixes of the alignment, called alignment-suffixes. An alignment-suffix represents one suffix of a string or suffixes of multiple strings starting at the same position in the alignment. The suffix tree of alignment makes good use of similarity in strings theoretica...

We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the suffix tree based approaches for the repeat finding problem, being particularly well suited for very large inputs. We prove the corrrectness and complexity of th...

The suffix effect--the loss of recency induced by a redundant end-of-list item--was studied in a visuospatial serial recall task involving the memory for the position of dots on a screen. A visuospatial suffix markedly impaired recall of the last to-be-remembered dot. The impact on recall was roughly of equal magnitude whether the suffix shared attributes with the to-be-remembered dots (Experim...

The present study explores learning phonological alternations that contain exceptions. Participants were exposed to a back/round vowel harmony pattern in which a regular suffix followed harmony, varying between /e/ and /o/ depending on the back/round phonetic features of the stem, and an exceptional suffix that was always /o/ regardless of the features of the stem vowel. Participants in Experim...

The suffix array is a compact representation of the lexicographic ordering of the suffixes of a text [1]. Each element of the array is an index into the original string; SAX [i] = j indicates that the suffix starting at position j in T is the i-th lowest suffix in X. As an example consider the string T = AGATCGATA$. The suffix array of T is SAT = [10, 9, 1, 7, 3, 5, 6, 2, 8, 4]. As the suffix a...

Suffix arrays and LCP arrays are one of the most fundamental data structures widely used for various kinds of string processing. Many problems can be solved efficiently by using suffix arrays, or a pair of suffix arrays and LCP arrays. In this paper, we consider two problems for a string of length N , the characters of which are represented as integers in [1, . . . , σ] for 1 ≤ σ ≤ N ; the stri...

Suffix trees are highly regarded data structures for text indexing and string algorithms [MCreight 76, Weiner 73]. For any given string w of length n = |w|, a suffix tree for w takes O(n) nodes and links. It is often presented as a compacted version of a suffix trie for w, where the latter is the trie (or digital search tree) built on the suffixes of w. Here the compaction process replaces each...

We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings A and B is a compacted trie representing all suffixes in A and B. It has |A|+ |B| leaves and can be constructed in O(|A|+ |B|) time. However, if the two strings are similar, the generalized suffix tree is not efficient because it does not ex...

This thesis presents a new approach for linear-time suffix sorting. It introduces a new sorting principle that can be used to build the first non-recursive linear-time suffix array construction algorithm named GSACA. Although GSACA cannot hold up with the performance of state of the art suffix array construction algorithms, the algorithm introduces a lot of new ideas for suffix array constructi...

Separate conserved copies of suffix, a short interspersed Drosophila retroelement (SINE), and also divergent copies in the 3' untranslated regions of the three genes, have already been described. Suffix has also been identified on the 3' end of the Drosophila non-LTR F element, where it forms the last conserved domain of the reverse transcriptase (RT). In our current study, we show that the sep...