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Keyword

alignment-free methods

Description: Computational approaches for comparing or analyzing biological sequences without constructing explicit sequence alignments.
OpenAlex ID: keywords/alignment-free-methods
Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes
2012 · Jérémy Desaphy, Karima Azdimousa, et al. · Journal of Chemical Information and Modeling · 155
DeepFam: deep learning based alignment-free method for protein family modeling and prediction
2018 · Seokjun Seo, Minsik Oh, et al. · Bioinformatics · 134
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Co-phylog: an assembly-free phylogenomic approach for closely related organisms
2013 · Huiguang Yi, Li Jin · Nucleic Acids Research · 132
Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics
2021 · Congyu Lu, Zheng Zhang, et al. · BMC Biology · 130
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FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
2014 · Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, et al. · PeerJ · 109
The perils of plenty: what are we going to do with all these genes?
2008 · Allen Rodrigo, Frederic Bertels, et al. · Philosophical Transactions of the Royal Society B Biological Sciences · 97
MeShClust: an intelligent tool for clustering DNA sequences
2018 · Benjamin T James, Brian B Luczak, et al. · Nucleic Acids Research · 96
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Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny?
2007 · Michael Höhl, Mark A. Ragan · Systematic Biology · 95
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles
2022 · Quang-Hien Kha, Quang-Thai Ho, et al. · Journal of Chemical Information and Modeling · 86
Topology comparison of Twitter diffusion networks effectively reveals misleading information
2020 · Francesco Pierri, Carlo Piccardi, et al. · Scientific Reports · 81
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Efficient alignment-free DNA barcode analytics
2009 · Pavel Kuksa, Vladimir Pavlovic · BMC Bioinformatics · 79
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Proper evaluation of alignment-free network comparison methods
2015 · Ömer Nebil Yaveroğlu, Tijana Milenković, et al. · Bioinformatics · 72
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A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering
2014 · Changchuan Yin, Ying Chen, et al. · Journal of Theoretical Biology · 71
Fast and accurate phylogeny reconstruction using filtered spaced-word matches
2016 · Chris-André Leimeister, Salma Sohrabi-Jahromi, et al. · Bioinformatics · 69
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An alignment-free method to find similarity among protein sequences via the general form of Chou’s pseudo amino acid composition
2013 · M.K. Gupta, R. Niyogi, et al. · SAR and QSAR in environmental research · 67
A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition
2017 · Pooja Tripathi, Paras N. Pandey · Journal of Theoretical Biology · 64
Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
2021 · Michael Sheinman, Ksenia Arkhipova, et al. · eLife · 61
Estimating evolutionary distances between genomic sequences from spaced-word matches
2015 · Burkhard Morgenstern, Bingyao Zhu, et al. · Algorithms for Molecular Biology · 60
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ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels
2019 · Gurjit S. Randhawa, Kathleen A. Hill, et al. · BMC Genomics · 59
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Editorial: Alignment-free methods in computational biology
2014 · S. Vinga · Briefings in Bioinformatics · 59
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Efficient estimation of pairwise distances between genomes
2009 · Mirjana Domazet-Lošo, Bernhard Haubold · Bioinformatics · 57
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Alignment-free detection of local similarity among viral and bacterial genomes
2011 · Mirjana Domazet-Lošo, Bernhard Haubold · Bioinformatics · 56
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Probabilistic topic modeling for the analysis and classification of genomic sequences
2015 · Massimo La Rosa, Antonino Fiannaca, et al. · BMC Bioinformatics · 53
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Proteomic applications of automated GPCR classification
2007 · Matthew N. Davies, David E. Gloriam, et al. · PROTEOMICS · 51
RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
2014 · Zhaojun Zhang, Wei Wang · Bioinformatics · 48
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Works count: 363
Citation count: 3,899
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