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   Articles with "sequence alignment" as a keyword



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Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP.

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recommendations! Published in 2021 at "Methods in molecular biology"

DOI: 10.1007/978-1-0716-1036-7_7

Abstract: The estimation of very large multiple sequence alignments is a challenging problem that requires special techniques in order to achieve high accuracy. Here we describe two software packages-PASTA and UPP-for constructing alignments on large and… read more here.

Keywords: sequence alignment; multiple sequence; alignment large; pasta upp ... See more keywords

PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization

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recommendations! Published in 2022 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.1c01360

Abstract: Therapeutic peptides offer potential advantages over small molecules in terms of selectivity, affinity, and their ability to target "undruggable" proteins that are associated with a wide range of pathologies. Despite their importance, current molecular design… read more here.

Keywords: visualization; peptide sequence; sequence alignment; pepsea ... See more keywords

Evaluating the significance of embedding-based protein sequence alignment with clustering and double dynamic programming for remote homology

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recommendations! Published in 2025 at "Scientific Reports"

DOI: 10.1038/s41598-025-23319-x

Abstract: Accurate detection of protein sequence homology is essential for understanding evolutionary relationships and predicting protein functions, particularly for detecting remote homology in the “twilight zone” (20-35% sequence similarity), where traditional sequence alignment methods often fail.… read more here.

Keywords: remote homology; sequence alignment; dynamic programming; homology ... See more keywords

A survey on the algorithm and development of multiple sequence alignment

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac069

Abstract: Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can reveal the potential information in biological sequences, such as function, evolution and structure. MSA is widely used in many bioinformatics scenarios, such as… read more here.

Keywords: sequence alignment; msa; multiple sequence; alignment ... See more keywords

Ggmsa: a Visual Exploration Tool for Multiple Sequence Alignment and Associated Data

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac222

Abstract: The identification of the conserved and variable regions in the multiple sequence alignment (MSA) is critical to accelerating the process of understanding the function of genes. MSA visualizations allow us to transform sequence features into… read more here.

Keywords: associated data; sequence alignment; sequence; multiple sequence ... See more keywords

WMSA 2: a multiple DNA/RNA sequence alignment tool implemented with accurate progressive mode and a fast win-win mode combining the center star and progressive strategies.

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recommendations! Published in 2023 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbad190

Abstract: Multiple sequence alignment is widely used for sequence analysis, such as identifying important sites and phylogenetic analysis. Traditional methods, such as progressive alignment, are time-consuming. To address this issue, we introduce StarTree, a novel method… read more here.

Keywords: time; win win; sequence alignment; sequence ... See more keywords

Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm

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recommendations! Published in 2018 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btx643

Abstract: Abstract Motivation Pair Hidden Markov Models (PHMMs) are probabilistic models used for pairwise sequence alignment, a quintessential problem in bioinformatics. PHMMs include three types of hidden states: match, insertion and deletion. Most previous studies have… read more here.

Keywords: hidden states; beyond similarity; similarity assessment; sequence alignment ... See more keywords

Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.

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recommendations! Published in 2023 at "Nucleic acids research"

DOI: 10.1093/nar/gkad400

Abstract: The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these… read more here.

Keywords: sequence alignment; immune repertoires; multiple sequence; alignment ... See more keywords
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Measuring Phylogenetic Information of Incomplete Sequence Data.

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recommendations! Published in 2021 at "Systematic biology"

DOI: 10.1093/sysbio/syab073

Abstract: Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of… read more here.

Keywords: information; model misspecification; measuring phylogenetic; sequence alignment ... See more keywords

Enhanced Quantum-Based DNA Sequence Alignment With Noise Handling and Error Detection

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recommendations! Published in 2025 at "IEEE Access"

DOI: 10.1109/access.2025.3632898

Abstract: This paper presents an enhanced quantum computing approach for DNA sequence alignment, integrating advanced noise management and robust error detection. We augment existing quantum alignment methodologies by incorporating supplementary qubits for each base, enabling improved… read more here.

Keywords: sequence alignment; error detection; sequence; error ... See more keywords

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

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recommendations! Published in 2020 at "IEEE Transactions on Computers"

DOI: 10.1109/tc.2020.3041402

Abstract: Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As… read more here.

Keywords: performance energy; energy savings; energy; sequence alignment ... See more keywords