scholarly journals Engineering Augmented Suffix Sorting Algorithms

2018 ◽  
Author(s):  
Felipe A. Louza ◽  
Guilherme P. Telles ◽  
Simon Gog
Keyword(s):  
Computer Science ◽  
Full Text ◽  
Suffix Array ◽  
Optimal Time ◽  
Time And Space ◽  
Sorting Algorithms ◽  
Constant Size ◽  
Common Prefix ◽  
Efficient Processing ◽  
Burrows Wheeler Transform

Strings are prevalent in Computer Science and algorithms for their efficient processing are fundamental in various applications. The results introduced in this work contribute with theoretical improvements and practical advances in building full-text indexes. Our first contribution is an in-place algorithm that computes the Burrows-Wheeler transform and the longest common prefix (LCP) array. Our second contribution is the construction of the suffix array augmented with the LCP array in optimal time and space for strings from constant size alphabets. Our third contribution is a set of algorithms to construct full-text indexes for string collections in optimal theoretical bounds. This work is an extended abstract of the Ph.D. thesis of the first author.

An Efficient Tool for Searching Maximal and Super Maximal Repeats in Large DNA/Protein Sequences via Induced-Enhanced Suffix Array

2019 ◽  
Vol 12 (2) ◽  
pp. 128-134
Author(s):  
Sanjeev Kumar ◽  
Suneeta Agarwal ◽  
Ranvijay
Keyword(s):  
Protein Sequences ◽  
Input Sequence ◽  
Suffix Array ◽  
Secondary Memory ◽  
Time And Space ◽  
Efficient Tool ◽  
Frequency Distributions ◽  
Alignment Algorithms ◽  
Common Prefix ◽  
Art Works

Background: DNA and Protein sequences of an organism contain a variety of repeated structures of various types. These repeated structures play an important role in Molecular biology as they are related to genetic backgrounds of inherited diseases. They also serve as a marker for DNA mapping and DNA fingerprinting. Efficient searching of maximal and super maximal repeats in DNA/Protein sequences can lead to many other applications in the area of genomics. Moreover, these repeats can also be used for identification of critical diseases by finding the similarity between frequency distributions of repeats in viruses and genomes (without using alignment algorithms). Objective: The study aims to develop an efficient tool for searching maximal and super maximal repeats in large DNA/Protein sequences. Methods: The proposed tool uses a newly introduced data structure Induced Enhanced Suffix Array (IESA). IESA is an extension of enhanced suffix array. It uses induced suffix array instead of classical suffix array. IESA consists of Induced Suffix Array (ISA) and an additional array-Longest Common Prefix (LCP) array. ISA is an array of all sorted suffixes of the input sequence while LCP array stores the lengths of the longest common prefixes between all pairs of consecutive suffixes in an induced suffix array. IESA is known to be efficient w.r.t. both time and space. It facilitates the use of secondary memory for constructing the large suffix-array. Results: An open source standalone tool named MSR-IESA for searching maximal and super maximal repeats in DNA/Protein sequences is provided at https://github.com/sanjeevalg/MSRIESA. Experimental results show that the proposed algorithm outperforms other state of the art works w.r.t. to both time and space. Conclusion: The proposed tool MSR-IESA is remarkably efficient for the analysis of DNA/Protein sequences, having maximal and super maximal repeats of any length. It can be used for identification of well-known diseases.

scholarly journals gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Felipe A. Louza ◽  
Guilherme P. Telles ◽  
Simon Gog ◽  
Nicola Prezza ◽  
Giovanna Rosone
Keyword(s):  
Data Structures ◽  
Suffix Array ◽  
Data Indexing ◽  
Related Data ◽  
Suffix Arrays ◽  
Common Prefix ◽  
Different Types ◽  
Single String ◽  
Burrows Wheeler Transform ◽  
Longest Common Prefix Array

Abstract Background The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows–Wheeler transform, and the document array, are often needed to accompany the suffix array to efficiently solve a wide variety of problems. While several algorithms have been proposed to construct the suffix array for a single string, less emphasis has been put on algorithms to construct suffix arrays for string collections. Result In this paper we introduce , an open source software for constructing the suffix array and related data indexing structures for a string collection with N symbols in O(N) time. Our tool is written in and is based on the algorithm gSACA-K (Louza et al. in Theor Comput Sci 678:22–39, 2017), the fastest algorithm to construct suffix arrays for string collections. The tool supports large fasta, fastq and text files with multiple strings as input. Experiments have shown very good performance on different types of strings. Conclusions is a fast, portable, and lightweight tool for constructing the suffix array and additional data structures for string collections.

scholarly journals Compact and hash based variants of the suffix array

2017 ◽  
Vol 65 (4) ◽  
pp. 407-418
Author(s):  
S. Grabowski ◽  
M. Raniszewski
Keyword(s):  
Data Structure ◽  
Full Text ◽  
Hash Table ◽  
Suffix Array ◽  
Fixed Size ◽  
Text Indexing ◽  
Text Length ◽  
Speed Up ◽  
Pattern Searches ◽  
Search Interval

AbstractFull-text indexing aims at building a data structure over a given text capable of efficiently finding arbitrary text patterns, and possibly requiring little space. We propose two suffix array inspired full-text indexes. One, called SA-hash, augments the suffix array with a hash table to speed up pattern searches due to significantly narrowed search interval before the binary search phase. The other, called FBCSA, is a compact data structure, similar to Mäkinen’s compact suffix array (MakCSA), but working on fixed size blocks. Experiments on the widely used Pizza & Chili datasets show that SA-hash is about 2–3 times faster in pattern searches (counts) than the standard suffix array, for the price of requiring 0.2n–1.1nbytes of extra space, wherenis the text length. FBCSA, in one of the presented variants, reduces the suffix array size by a factor of about 1.5–2, while it gets close in search times, winning in speed with its competitors known from the literature, MakCSA and LCSA.

Komparasi Algoritma Quicksort dan Bucket Sort pada Pengurutan Data Integer

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Audy Audy
Keyword(s):  
Data Type ◽  
Minimum Amount ◽  
Time And Space ◽  
Worst Case ◽  
Sorting Algorithms ◽  
Program Complexity ◽  
Data Sorting ◽  
Case Condition

Data sorting is a technique that widely used as a part of a bigger process. Therefore, data sorting should not be the problem of program complexity. This paper gives the reader a comparison between two sorting algorithms, which are comparison based and non-comparison based, in time and space performance. The data type that used in this paper is an integer data type. Testing is carried out by using two types of data’s condition, which are the worst-case condition in each algorithm, and two amounts of data, which represent the maximum and minimum amount data.

A fraction activity to understand sorting algorithms

2017 ◽  
Vol 23 (9) ◽  
pp. 560-563
Author(s):  
Barbara King ◽  
Carmen Petrick Smith
Keyword(s):  
Computer Science ◽  
Student Interest ◽  
Science Students ◽  
Stem Fields ◽  
Link Type ◽  
Integrated Stem ◽  
Sorting Algorithms ◽  
Science Technology ◽  
And Mathematics ◽  
Mathematics Department

In an activity integrating mathematics and computer science, students order fractions from least to greatest, reflect on the process they used, and make connections to sorting algorithms. Contributors to the iSTEM (Integrating Science, Technology, Engineering, and Mathematics) department share ideas and activities that stimulate student interest in the integrated STEM fields in K–grade 6 classrooms. Send submissions of no more than 1500 words to this department by accessing http://tcm.msubmit.net. See detailed submission guidelines for all departments at http://www.nctm.org/WriteForTCM.

scholarly journals Sliding Suffix Tree

Algorithms ◽  
2018 ◽  
Vol 11 (8) ◽  
pp. 118 ◽  
Author(s):  
Andrej Brodnik ◽  
Matevž Jekovec
Keyword(s):  
Data Structure ◽  
Suffix Tree ◽  
Sliding Window ◽  
Constant Time ◽  
Optimal Time ◽  
Constant Size ◽  
Query String

We consider a sliding window W over a stream of characters from some alphabet of constant size. We want to look up a pattern in the current sliding window content and obtain all positions of the matches. We present an indexed version of the sliding window, based on a suffix tree. The data structure of size Θ(|W|) has optimal time queries Θ(m+occ) and amortized constant time updates, where m is the length of the query string and occ is its number of occurrences.

scholarly journals RECONSTRUCTING A SUFFIX ARRAY

2006 ◽  
Vol 17 (06) ◽  
pp. 1281-1295 ◽  
Author(s):  
FRANTISEK FRANEK ◽  
WILLIAM F. SMYTH
Keyword(s):  
Data Compression ◽  
Data Structures ◽  
Suffix Tree ◽  
Suffix Array ◽  
Efficient Algorithms ◽  
Lexicographical Order ◽  
Time And Space

For certain problems (for example, computing repetitions and repeats, data compression applications) it is not necessary that the suffixes of a string represented in a suffix tree or suffix array should occur in lexicographical order (lexorder). It thus becomes of interest to study possible alternate orderings of the suffixes in these data structures, that may be easier to construct or more efficient to use. In this paper we consider the "reconstruction" of a suffix array based on a given reordering of the alphabet, and we describe simple time- and space-efficient algorithms that accomplish it.

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