Related papers: A Novel Method for Comparative Analysis of DNA Seq…
Detection transformers have recently shown promising object detection results and attracted increasing attention. However, how to develop effective domain adaptation techniques to improve its cross-domain performance remains unexplored and…
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…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…
Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…
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…
To handle time series with complicated oscillatory structure, we propose a novel time-frequency (TF) analysis tool that fuses the short time Fourier transform (STFT) and periodic transform (PT). Since many time series oscillate with…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
To solve the range cell migration (RCM) and spectrum spread during the integration time induced by the motion of a target, this paper proposes a new coherent integration method based on Radon non-uniform FRFT (NUFRFT) for random pulse…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
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…
We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree.…
Motivation: Alignment-free distance and similarity functions (AF functions, for short) are a well established alternative to two and multiple sequence alignments for many genomic, metagenomic and epigenomic tasks. Due to data-intensive…
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…