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   Articles with "alignment free" as a keyword



Sequence Comparison Without Alignment: The SpaM Approaches.

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

DOI: 10.1007/978-1-0716-1036-7_8

Abstract: Sequence alignment is at the heart of DNA and protein sequence analysis. For the data volumes that are nowadays produced by massively parallel sequencing technologies, however, pairwise and multiple alignment methods are often too slow.… read more here.

Keywords: approaches sequence; word; sequence comparison; alignment free ... See more keywords

An alignment-free measure based on physicochemical properties of amino acids for protein sequence comparison

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recommendations! Published in 2019 at "Computational biology and chemistry"

DOI: 10.1016/j.compbiolchem.2019.01.005

Abstract: Sequence comparison is an important topic in bioinformatics. With the exponential increase of biological sequences, the traditional protein sequence comparison methods - the alignment methods become limited, so the alignment-free methods are widely proposed in… read more here.

Keywords: sequence comparison; physicochemical properties; protein sequence; alignment free ... See more keywords

Alignment-free solvent-enabled automatic packaging for thermoplastic microfluidics

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recommendations! Published in 2025 at "Journal of Micromechanics and Microengineering"

DOI: 10.1088/1361-6439/ada61b

Abstract: As the demands in function versatility, integration density and mass manufacturability grow, multilayer thermoplastic microfluidic devices with sophisticated structures have rapidly gained interests. Yet, great challenges persist in packaging process, namely alignment and sealing of… read more here.

Keywords: solvent; solvent enabled; alignment free; free solvent ... See more keywords

Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings

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recommendations! Published in 2023 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbac599

Abstract: Abstract Protein language modeling is a fast-emerging deep learning method in bioinformatics with diverse applications such as structure prediction and protein design. However, application toward estimating sequence conservation for functional site prediction has not been… read more here.

Keywords: functional sites; sequence conservation; alignment free; conservation ... See more keywords
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Alignment-free inference of hierarchical and reticulate phylogenomic relationships

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recommendations! Published in 2019 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbx067

Abstract: Abstract We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows… read more here.

Keywords: inference hierarchical; hierarchical reticulate; free inference; alignment free ... See more keywords

The super‐n‐motifs model: a novel alignment‐free approach for representing and comparing RNA secondary structures

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recommendations! Published in 2017 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btw773

Abstract: Motivation: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take… read more here.

Keywords: rna secondary; secondary structures; motifs model; alignment free ... See more keywords

SENSE: Siamese neural network for sequence embedding and alignment-free comparison

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recommendations! Published in 2019 at "Bioinformatics"

DOI: 10.1093/bioinformatics/bty887

Abstract: MOTIVATION Sequence analysis is arguably a foundation of modern biology. Classic approaches to sequence analysis are based on sequence alignment, which is limited when dealing with large-scale sequence data. A dozen of alignment-free approaches have… read more here.

Keywords: neural network; sequence; sense siamese; alignment free ... See more keywords

Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences

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recommendations! Published in 2019 at "GigaScience"

DOI: 10.1093/gigascience/giy148

Abstract: Abstract Word-based or ‘alignment-free’ sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate… read more here.

Keywords: whole proteome; spam fast; proteome sequences; prot spam ... See more keywords
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Seeker: alignment-free identification of bacteriophage genomes by deep learning.

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recommendations! Published in 2020 at "Nucleic acids research"

DOI: 10.1093/nar/gkaa856

Abstract: Recent advances in metagenomic sequencing have enabled discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a… read more here.

Keywords: free identification; deep learning; seeker; bacteriophage ... See more keywords

A Ka-Band Single-Layer Optically Transparent Transmitarray With Diffusive Radiation for Alignment-Free Indoor Multipoint Communication

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recommendations! Published in 2025 at "IEEE Antennas and Wireless Propagation Letters"

DOI: 10.1109/lawp.2025.3596036

Abstract: This letter presents a glass-based uniform multibeam transparent transmitarray that achieves a highly diffusive and uniform radiation pattern over a wide angular range, and supports dual-polarization to enable simultaneous multidirectional coverage for multiuser mmWave communication.… read more here.

Keywords: single layer; radiation; alignment free; transparent transmitarray ... See more keywords

Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective

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recommendations! Published in 2022 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"

DOI: 10.1109/tcbb.2022.3140873

Abstract: The encounter of large amounts of biological sequence data generated during the last decades and the algorithmic and hardware improvements have offered the possibility to apply machine learning techniques in bioinformatics. While the machine learning… read more here.

Keywords: alignment free; machine learning; sequence; sequence comparison ... See more keywords