Related papers: New Sequence Alignment Algorithm using AI Rules an…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
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…
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…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
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…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
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…
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…
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…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
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…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. A standard approach to speed up this task is to compute "sketches" of the DNA reads (typically via…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
Social network alignment, aligning different social networks on their common users, is receiving dramatic attention from both academic and industry. All existing studies consider the social network to be static and neglect its inherent…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…