Sequence Comparison Without Alignment: The SpaM Approaches.
Sign Up to like & getrecommendations! 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
Sign Up to like & getrecommendations! 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 estimation of sequence conservation for identifying functional sites using protein sequence embeddings
Sign Up to like & getrecommendations! 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
Alignment-free inference of hierarchical and reticulate phylogenomic relationships
Sign Up to like & getrecommendations! 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
Sign Up to like & getrecommendations! 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
Sign Up to like & getrecommendations! 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
Sign Up to like & getrecommendations! 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
Seeker: alignment-free identification of bacteriophage genomes by deep learning.
Sign Up to like & getrecommendations! 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
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective
Sign Up to like & getrecommendations! 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
Adaptation of Pair-Polar Structures to Compute a Secure and Alignment-Free Fingerprint Template
Sign Up to like & getrecommendations! Published in 2023 at "IEEE Transactions on Industrial Informatics"
DOI: 10.1109/tii.2022.3195938
Abstract: The unalterable nature of fingerprint biometrics leads to permanent identity loss of a user if an original fingerprint template is compromised. Moreover, it is evident in the literature that reconstructing a fingerprint image from an… read more here.
Keywords: free fingerprint; fingerprint template; alignment free; fingerprint ... See more keywords
Alignment-free sequence comparison: benefits, applications, and tools
Sign Up to like & getrecommendations! Published in 2017 at "Genome Biology"
DOI: 10.1186/s13059-017-1319-7
Abstract: Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them… read more here.
Keywords: benefits applications; sequence comparison; comparison benefits; alignment free ... See more keywords