ArticleBioinformatics (Oxford, England)2016
Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 27 citations in OpenAlex.
- A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Reservoir hosts prediction for COVID-19 by hybrid transfer learning model.Journal of biomedical informatics · 2021Article
- Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples.Frontiers in microbiology · 2021Article
- Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data.Quantitative biology (Beijing, China) · 2020Article
- A network-based integrated framework for predicting virus-prokaryote interactions.NAR genomics and bioinformatics · 2020Article
- A new statistic for efficient detection of repetitive sequences.Bioinformatics (Oxford, England) · 2019Article
- Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA.BMC genomics · 2018Article
- Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences.Scientific reports · 2018Article
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.Frontiers in microbiology · 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
- kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.PLoS computational biology · 2017Article
- VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.Microbiome · 2017Article
- CAFE: aCcelerated Alignment-FrEe sequence analysis.Nucleic acids research · 2017Article
- Prediction of virus-host infectious association by supervised learning methods.BMC bioinformatics · 2017Article
- Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.Nucleic acids research · 2017Article
- Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.Scientific reports · 2016Article
- Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.Scientific reports · 2016Article
- Moderate Genetic Diversity and Genetic Differentiation in the Relict TreeFrontiers in plant science · 2016Article
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
Abstract
motivationNext-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.A plausible model for this underlying distribution of word counts is given through modeling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data.
resultsHere we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution ,: using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate those using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results ,: and that the clustering results that use a N: MC of the estimated order give a plausible clustering of the species. AVAILABILITY AND IMPLEMENTATION: Our implementation of the statistics developed here is available as R package 'NGS.MC' at http://www-rcf.usc.edu/∼fsun/Programs/NGS-MC/NGS-MC.html CONTACT: fsun@usc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.