相关论文: Probabilistic pairwise sequence alignment
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…
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…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
From molecular imaging to wireless communications, the ability to align and reconstruct signals from multiple misaligned observations is crucial for system performance. We study the problem of multi-reference alignment (MRA), which arises…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
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…
We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise…
Analyzing the relation between a set of biological sequences can help to identify and understand the evolutionary history of these sequences and the functional relations among them. Multiple Sequence Alignment (MSA) is the main obstacle to…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon…
Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments (MSAs) and phylogenetic trees of large datasets.…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
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…
Advances in bio-technology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications…
Semantic matching is of central importance to many natural language tasks \cite{bordes2014semantic,RetrievalQA}. A successful matching algorithm needs to adequately model the internal structures of language objects and the interaction…