Papers Multiple Sequence Alignment
“Multiple Sequence Alignment” 태그가 달린 논문 62편 · 필터 해제
Align-RUDDER: Learning From Few Demonstrations by Reward Redistribution
Reinforcement learning algorithms require many samples when solving complex hierarchical tasks with sparse and delayed rewards. For such complex tasks, the recently proposed RUDDER uses reward redistribution to leverage …
General Reinforcement LearningMinecraftMultiple Sequence AlignmentSafe ExplorationNeural Time Warping For Multiple Sequence Alignment
Multiple sequences alignment (MSA) is a traditional and challenging task for time-series analyses. The MSA problem is formulated as a discrete optimization problem and is typically solved by dynamic programming. However,…
Multiple Sequence AlignmentTime SeriesTime Series AnalysisAccurate Protein Structure Prediction by Embeddings and Deep Learning Representations
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental …
Deep LearningDrug DesignMultiple Sequence AlignmentPrediction+1Boltzmann machine learning and regularization methods for inferring evolutionary fields and couplings from a multiple sequence alignment
The inverse Potts problem to infer a Boltzmann distribution for homologous protein sequences from their single-site and pairwise amino acid frequencies recently attracts a great deal of attention in the studies of protei…
BIG-bench Machine LearningMultiple Sequence AlignmentSeq-SetNet: Exploring Sequence Sets for Inferring Structures
Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural in…
Multiple Sequence AlignmentProtein Secondary Structure PredictionProtein Structure PredictionPrivacy Preserving Location Data Publishing: A Machine Learning Approach
Publishing datasets plays an essential role in open data research and promoting transparency of government agencies. However, such data publication might reveal users' private information. One of the most sensitive sourc…
BIG-bench Machine LearningClusteringMultiple Sequence AlignmentPrivacy Preserving+1Influence of Multiple Sequence Alignment Depth on Potts Statistical Models of Protein Covariation
Potts statistical models have become a popular and promising way to analyze mutational covariation in protein Multiple Sequence Alignments (MSAs) in order to understand protein structure, function and fitness. But the st…
Multiple Sequence AlignmentMultiple Sequence Alignment is not a Solved Problem
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, …
Multiple Sequence AlignmentOptimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network
A profile comparison method with position-specific scoring matrix (PSSM) is one of the most accurate alignment methods. Currently, cosine similarity and correlation coefficient are used as scoring functions of dynamic pr…
Multiple Sequence AlignmentFull Reconstruction of Non-Stationary Strand-Symmetric Models on Rooted Phylogenies
Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events…
Multiple Sequence AlignmentQuickProbs 2: towards rapid construction of high-quality alignments of large protein families
Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet. As we show, well-established techniques emplo…
Multiple Sequence AlignmentAligning 415 519 proteins in less than two hours on PC
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence…
Multiple Sequence AlignmentVocal Bursts Valence PredictionIdentifying relevant positions in proteins by Critical Variable Selection
Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underl…
Multiple Sequence AlignmentVariable SelectionStatistically-Consistent k-mer Methods for Phylogenetic Tree Reconstruction
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean d…
Multiple Sequence AlignmentPredicting diverse M-best protein contact maps
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which pr…
Multiple Sequence AlignmentMultiple sequence alignment for short sequences
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 prac…
Multiple Sequence AlignmentLiquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction
The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract "direct" correlations between distant sites that are latent in "indirect" correlations observed in a protein mul…
Multiple Sequence AlignmentPredictionProtein Structure PredictionUltra-large alignments using Phylogeny-aware Profiles
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 l…
BIG-bench Machine LearningMultiple Sequence AlignmentA Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform
Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are …
ClusteringMultiple Sequence AlignmentMRFalign: Protein Homology Detection through Alignment of Markov Random Fields
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) …
Multiple Sequence Alignment