Related papers: Linear-Time Sequence Comparison Using Minimal Abse…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their…
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…
In this paper we introduce a method to detect words or phrases in a given sequence of alphabets without knowing the lexicon. Our linear time unsupervised algorithm relies entirely on statistical relationships among alphabets in the input…
A minimal absent word of a sequence x, is a sequence yt hat is not a factorof x, but all of its proper factors are factors of x as well. The set of minimal absent words uniquely defines the sequence itself. In recent times minimal absent…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
Given a string $w$, another string $v$ is said to be a subsequence of $w$ if $v$ can be obtained from $w$ by removing some of its letters; on the other hand, $v$ is called an absent subsequence of $w$ if $v$ is not a subsequence of $w$. The…
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…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
An absent factor of a string $w$ is a string $u$ which does not occur as a contiguous substring (a.k.a. factor) inside $w$. We extend this well-studied notion and define absent subsequences: a string $u$ is an absent subsequence of a string…
A novel non-linear approach to fast and effective comparison of sequences is presented, compared to the traditional cross-correlation operator, and illustrated with respect to DNA sequences.
This paper proposes an algorithm for alignment-free sequence comparison using Logical Match. Here, we compute the score using fuzzy membership values which generate automatically from the number of matches and mismatches. We demonstrate the…
Minimal-interval semantics associates with each query over a document a set of intervals, called witnesses, that are incomparable with respect to inclusion (i.e., they form an antichain): witnesses define the minimal regions of the document…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
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…
Many NLP tasks including machine comprehension, answer selection and text entailment require the comparison between sequences. Matching the important units between sequences is a key to solve these problems. In this paper, we present a…