Papers Multiple Sequence Alignment
“Multiple Sequence Alignment” 태그가 달린 논문 62편 · 필터 해제
High Performance Multiple Sequence Alignment Algorithms for Comparison of Microbial Genomes
Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global …
Multiple Sequence AlignmentAligning Speakers: Evaluating and Visualizing Text-based Diarization Using Efficient Multiple Sequence Alignment (Extended Version)
This paper presents a novel evaluation approach to text-based speaker diarization (SD), tackling the limitations of traditional metrics that do not account for any contextual information in text. Two new metrics are prop…
Multiple Sequence Alignmentspeaker-diarizationSpeaker DiarizationPEvoLM: Protein Sequence Evolutionary Information Language Model
With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary informa…
Language ModelingLanguage ModellingmodelMultiple Sequence Alignment+2PoET: A generative model of protein families as sequences-of-sequences
Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must …
Language ModellingMultiple Sequence AlignmentTransfer LearningEnhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation
The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein str…
Language ModelingLanguage ModellingMultiple Sequence AlignmentProtein Folding+1Convolutional ProteinUnetLM competitive with long short-term memory-based protein secondary structure predictors
The protein secondary structure (SS) prediction plays an important role in the characterization of general protein structure and function. In recent years, a new generation of algorithms for SS prediction based on embedd…
Multiple Sequence AlignmentPredictionProtein Secondary Structure PredictionUNET SegmentationSmall Coupling Expansion for Multiple Sequence Alignment
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 …
Multiple Sequence AlignmentPairwise sequence alignment at arbitrarily large evolutionary distance
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 …
Multiple Sequence AlignmentApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequences. In pHMMs, sequences are represented…
CPUGPUMultiple Sequence AlignmentExploring evolution-aware & -free protein language models as protein function predictors
Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI syste…
Multiple Sequence AlignmentPredictionFew Shot Protein Generation
We present the MSA-to-protein transformer, a generative model of protein sequences conditioned on protein families represented by multiple sequence alignments (MSAs). Unlike existing approaches to learning generative mod…
Multiple Sequence AlignmentUn nouvel algorithme pour la detection des transferts horizontaux de genes partiels entre les especes et pour la classification des transferts inferes
In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given…
Multiple Sequence AlignmentPEACH Tree: A Multiple Sequence Alignment and Tree Display Tool for Epidemiologists
PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering i…
EpidemiologyMultiple Sequence AlignmentPre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model
Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of …
Language ModelingLanguage ModellingMultiple Sequence AlignmentRepresentation LearningApplication of Sequence Embedding in Protein Sequence-Based Predictions
In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired b…
Multiple Sequence AlignmentPositionPredictionNeural Distance Embeddings for Biological Sequences
The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approa…
Multiple Sequence AlignmentMNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences
Abstract Summary Genomic sequences are widely used to infer the evolutionary history of a given group of individuals. Many methods have been developed for sequence clustering and tree building. In the early days of g…
Multiple Sequence AlignmentMSA Transformer
Unsupervised protein language models trained across millions of diverse sequences learn structure and function of proteins. Protein language models studied to date have been trained to perform inference from individual s…
Language ModelingLanguage ModellingMasked Language ModelingMultiple Sequence Alignment+1DLPAlign: A Deep Learning based Progressive Alignment Method for Multiple Protein Sequences
This paper proposed a novel and straightforward approach to improve the accuracy of progressive multiple protein sequence alignment method. We trained a decision-making model based on the convolutional neural networks an…
Decision MakingMultiple Sequence AlignmentProtein Secondary Structure PredictionPairwise heuristic sequence alignment algorithm based on deep reinforcement learning
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. How…
Deep Reinforcement LearningMultiple Sequence Alignmentreinforcement-learningReinforcement Learning+1