ArticleNucleic acids research2014
Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Genomic similarity to quantitatively evaluate the reassortment potential of H7N9 with other subtypes of avian influenza viruses.Frontiers in cellular and infection microbiology · 2026Article
- Enhancing Taxonomic Categorization of DNA Sequences with Deep Learning: A Multi-Label Approach.Bioengineering (Basel, Switzerland) · 2023Article
- Interpreting alignment-free sequence comparison: what makes a score a good score?NAR genomics and bioinformatics · 2022Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Accurate reconstruction of viral genomes in human cells from short reads using iterative refinement.BMC genomics · 2022Article
- Sequence Comparison Without Alignment: The SpaM Approaches.Methods in molecular biology (Clifton, N.J.) · 2021Article
- An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction.BMC bioinformatics · 2020Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- SWeeP: representing large biological sequences datasets in compact vectors.Scientific reports · 2020Article
- Specificity Analysis of Genome Based on Statistically Identical K-Words With Same Base Combination.IEEE open journal of engineering in medicine and biology · 2020Article
- The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.PloS one · 2020Article
- Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage.BMC bioinformatics · 2019Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics.BMC bioinformatics · 2019Article
- Alignment-free inference of hierarchical and reticulate phylogenomic relationships.Briefings in bioinformatics · 2019Review
- Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.GigaScience · 2019Article
- Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.Bioinformatics (Oxford, England) · 2019Article
- Lipidome Evolution in Mammalian Tissues.Molecular biology and evolution · 2018Article
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- Reconstructing evolutionary trees in parallel for massive sequences.BMC systems biology · 2017Article
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7 authors.
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Abstract
In this article, we present a user-friendly web interface for two alignment-free sequence-comparison methods that we recently developed. Most alignment-free methods rely on exact word matches to estimate pairwise similarities or distances between the input sequences. By contrast, our new algorithms are based on inexact word matches. The first of these approaches uses the relative frequencies of so-called spaced words in the input sequences, i.e. words containing 'don't care' or 'wildcard' symbols at certain pre-defined positions. Various distance measures can then be defined on sequences based on their different spaced-word composition. Our second approach defines the distance between two sequences by estimating for each position in the first sequence the length of the longest substring at this position that also occurs in the second sequence with up to k mismatches. Both approaches take a set of deoxyribonucleic acid (DNA) or protein sequences as input and return a matrix of pairwise distance values that can be used as a starting point for clustering algorithms or distance-based phylogeny reconstruction. The two alignment-free programmes are accessible through a web interface at 'Göttingen Bioinformatics Compute Server (GOBICS)': http://spaced.gobics.de http://kmacs.gobics.de and the source codes can be downloaded.
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