Related papers: Geometric approach to string analysis: deviation f…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
We propose a general framework for converting global and local similarities between biological sequences to quasi-metrics. In contrast to previous works, our formulation allows asymmetric distances, originating from uneven weighting of…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
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…
Bioinformatics, which is now a well known field of study, originated in the context of biological sequence analysis. Recently graphical representation takes place for the research on DNA sequence. Research in biological sequence is mainly…
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…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
Analysis of large-scale sequential data has been one of the most crucial tasks in areas such as bioinformatics, text, and audio mining. Existing string kernels, however, either (i) rely on local features of short substructures in the…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…
Kernel methods are powerful tools in machine learning. They have to be computationally efficient. In this paper, we present a novel Geometric-based approach to compute efficiently the string subsequence kernel (SSK). Our main idea is that…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
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…
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…
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…