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This work focuses on the definition and study of the n-dimensional k-vector, an algorithm devised to perform orthogonal range searching in static databases with multiple dimensions. The methodology first finds the order in which to search…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
All-pairs similarity problem asks to find all vector pairs in a set of vectors the similarities of which surpass a given similarity threshold, and it is a computational kernel in data mining and information retrieval for several tasks. We…
A hierarchical scheme for clustering data is presented which applies to spaces with a high number of dimension ($N_{_{D}}>3$). The data set is first reduced to a smaller set of partitions (multi-dimensional bins). Multiple clustering…
In this paper, we revisit the problem of indexing multi-dimensional data in memory for the efficient support of multi-dimensional range queries and nearest neighbor queries. This is a classic problem in main-memory databases, where there is…
The multidimensional databases often use compression techniques in order to decrease the size of the database. This paper introduces a new method called difference sequence compression. Under some conditions, this new technique is able to…
Data mining is the task of discovering interesting patterns from large amounts of data. There are many data mining tasks, such as classification, clustering, association rule mining, and sequential pattern mining. Sequential pattern mining…
Nearest neighbor searching of large databases in high-dimensional spaces is inherently difficult due to the curse of dimensionality. A flavor of approximation is, therefore, necessary to practically solve the problem of nearest neighbor…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
Ordered set (and map) is one of the most used data type. In addition to standard set operations, like insert, delete and contains, it can provide set-set operations such as union, intersection, and difference. Each of these set-set…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
We examine the problem of searching sequentially for a desired real value (a key) within a sorted unbalanced three-dimensional finite real array. This classic problem can be viewed as determining the correct dimensional threshold function…
A sorted set (or map) is one of the most used data types in computer science. In addition to standard set operations, like Insert, Remove, and Contains, it can provide set-set operations such as Union,Intersection, and Difference. Each of…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore architectures or graphic boards. Three…