ArticleBioinformatics (Oxford, England)2014
Fast alignment-free sequence comparison using spaced-word frequencies.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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62 citing papers in PubMed.
- Alignment-free viral sequence classification at scale.BMC genomics · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms.BMC bioinformatics · 2024Article
- VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.Bioinformatics (Oxford, England) · 2024Article
- CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model.Frontiers in microbiology · 2024Article
- PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches.BMC bioinformatics · 2023Article
- Effects of spaced k-mers on alignment-free genotyping.Bioinformatics (Oxford, England) · 2023Article
- Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes.BMC biology · 2023Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Improving bioinformatics software quality through incorporation of software engineering practices.PeerJ. Computer science · 2022Article
- Identification of isolated or mixed strains from long reads: a challenge met onMicrobial genomics · 2021Article
- Sequence Comparison Without Alignment: The SpaM Approaches.Methods in molecular biology (Clifton, N.J.) · 2021Article
- An Information-Entropy Position-WeightedFrontiers in genetics · 2021Article
- Prostate cancer heterogeneity assessment with multi-regional sampling and alignment-free methods.NAR genomics and bioinformatics · 2020Article
- Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.Molecular ecology · 2020Article
- Information Theory in Computational Biology: Where We Stand Today.Entropy (Basel, Switzerland) · 2020Article
- Positional Correlation Natural Vector: A Novel Method for Genome Comparison.International journal of molecular sciences · 2020Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method.Entropy (Basel, Switzerland) · 2020Article
- SWeeP: representing large biological sequences datasets in compact vectors.Scientific reports · 2020Article
2 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
motivationAlignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free approaches work by comparing the word composition of sequences. A well-known problem with these methods is that neighbouring word matches are far from independent.
resultsTo reduce the statistical dependency between adjacent word matches, we propose to use 'spaced words', defined by patterns of 'match' and 'don't care' positions, for alignment-free sequence comparison. We describe a fast implementation of this approach using recursive hashing and bit operations, and we show that further improvements can be achieved by using multiple patterns instead of single patterns. To evaluate our approach, we use spaced-word frequencies as a basis for fast phylogeny reconstruction. Using real-world and simulated sequence data, we demonstrate that our multiple-pattern approach produces better phylogenies than approaches relying on contiguous words. AVAILABILITY AND IMPLEMENTATION: Our program is freely available at http://spaced.gobics.de/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.