ReviewBriefings in bioinformatics2014
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.
Review in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
75 citing papers in PubMed.
- Trial
- Estimation of substitution and indel rates via k-mer statistics.Algorithms for molecular biology : AMB · 2026Article
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- The gift of novelty: repeat-robust k-mer-based estimators of mutation rates.Bioinformatics (Oxford, England) · 2026Article
- The gift of novelty: repeat-robustbioRxiv : the preprint server for biology · 2026Article
- Estimation of substitution and indel rates viaAlgorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- Estimation of substitution and indel rates viabioRxiv : the preprint server for biology · 2025Article
- Article
- A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- The determinants of the rarity of nucleic and peptide short sequences in nature.NAR genomics and bioinformatics · 2024Article
- VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.Bioinformatics (Oxford, England) · 2024Article
- New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.BMC bioinformatics · 2023Article
- Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota.PloS one · 2023Article
- Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources.Frontiers in plant science · 2023Article
- Interpreting alignment-free sequence comparison: what makes a score a good score?NAR genomics and bioinformatics · 2022Article
- The Statistics ofJournal of computational biology : a journal of computational molecular cell biology · 2022Article
- Alignment-free comparison of metagenomics sequences via approximate string matching.Bioinformatics advances · 2022Article
- Article
- MPRAdecoder: Processing of the Raw MPRA Data WithFrontiers in genetics · 2021Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
With the development of next-generation sequencing (NGS) technologies, a large amount of short read data has been generated. Assembly of these short reads can be challenging for genomes and metagenomes without template sequences, making alignment-based genome sequence comparison difficult. In addition, sequence reads from NGS can come from different regions of various genomes and they may not be alignable. Sequence signature-based methods for genome comparison based on the frequencies of word patterns in genomes and metagenomes can potentially be useful for the analysis of short reads data from NGS. Here we review the recent development of alignment-free genome and metagenome comparison based on the frequencies of word patterns with emphasis on the dissimilarity measures between sequences, the statistical power of these measures when two sequences are related and the applications of these measures to NGS data.
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Registered trials
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.