ArticleBioinformatics (Oxford, England)2012
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.Nature communications · 2024Article
- Interpreting alignment-free sequence comparison: what makes a score a good score?NAR genomics and bioinformatics · 2022Article
- HLMethy: a machine learning-based model to identify the hidden labels of mPlant molecular biology · 2019Article
- A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.Briefings in bioinformatics · 2019Article
- Alignment-free inference of hierarchical and reticulate phylogenomic relationships.Briefings in bioinformatics · 2019Review
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- Optimal choice of word length when comparing two Markov sequences using a χBMC genomics · 2017Article
- Alignment-free sequence comparison: benefits, applications, and tools.Genome biology · 2017Review
- Prediction of virus-host infectious association by supervised learning methods.BMC bioinformatics · 2017Article
- Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.Bioinformatics (Oxford, England) · 2016Article
- On the comparison of regulatory sequences with multiple resolution Entropic Profiles.BMC bioinformatics · 2016Article
- Clustering of reads with alignment-free measures and quality values.Algorithms for molecular biology : AMB · 2015Article
- Inferring phylogenies of evolving sequences without multiple sequence alignment.Scientific reports · 2014Article
- Robust k-mer frequency estimation using gapped k-mers.Journal of mathematical biology · 2014Article
- Fast alignment-free sequence comparison using spaced-word frequencies.Bioinformatics (Oxford, England) · 2014Article
- Global view of enhancer-promoter interactome in human cells.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.Briefings in bioinformatics · 2014Review
- Evolutionary conservation of the eumetazoan gene regulatory landscape.Genome research · 2014Article
- Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.BMC bioinformatics · 2014Article
- The distribution of word matches between Markovian sequences with periodic boundary conditions.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
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4 authors.
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Abstract
motivationThe identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets.
resultsWe present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods. We explore the usefulness of adding reverse complement words as well as words including mismatches into the neighbourhood. On simulated enhancer sequences as well as functional enhancers in mouse development, N2 is shown to outperform previous alignment-free measures. N2 is flexible, faster than competing methods and less susceptible to single sequence noise and the occurrence of repetitive sequences. Experiments on the mouse enhancers reveal that enhancers active in different tissues can be separated by pairwise comparison using N2.
conclusionN2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences. AVAILABILITY: The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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