An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

Pratas, Diogo; Silva, Raquel M.; Pinho, Armando J.; Ferreira, Paulo J. S. G.

doi:10.1038/srep10203

Cited by 31 publications

(24 citation statements)

References 62 publications

(62 reference statements)

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“…Boxes based on these bars have been drawn on the correlation heatmap. The linearly conserved regions, identified by our method as diagonals in a correlation heatmap, seem to be comparable to the results of [26]. This illustrates and confirms the functionality of our methods for large sequences.…”

Section: Resultssupporting

confidence: 83%

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

Sievers

Bosiek

Bisch

et al. 2017

Genes

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In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard k-mer analysis.

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Section: Resultssupporting

confidence: 83%

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

Sievers

Bosiek

Bisch

et al. 2017

Genes

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“…Also, retrieving Single Nucleotide Polymorphisms (SNP) data-detecting and localizing one base mutations on genomic data [160]. Other application is aligning DNA sequences using compression [161]; Using data compression to detect large transformations between the DNA of different individuals or species, also known as rearrangement detection, has also been shown to work efficiently [162]; It has also been used for efficient storage of data structures in pan-genome analysis, namely using de Bruijn graphs [163,164]. Here, the problem is to deal with large amounts of information and its fast retrieval.…”

Section: Discussionmentioning

confidence: 99%

A Survey on Data Compression Methods for Biological Sequences

2016

Self Cite

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Abstract:The ever increasing growth of the production of high-throughput sequencing data poses a serious challenge to the storage, processing and transmission of these data. As frequently stated, it is a data deluge. Compression is essential to address this challenge-it reduces storage space and processing costs, along with speeding up data transmission. In this paper, we provide a comprehensive survey of existing compression approaches, that are specialized for biological data, including protein and DNA sequences. Also, we devote an important part of the paper to the approaches proposed for the compression of different file formats, such as FASTA, as well as FASTQ and SAM/BAM, which contain quality scores and metadata, in addition to the biological sequences. Then, we present a comparison of the performance of several methods, in terms of compression ratio, memory usage and compression/decompression time. Finally, we present some suggestions for future research on biological data compression.

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“…Our implementation uses soft blending of Markov models with several orders. It has been shown that these models, working in cooperation, are very powerful, being superior to state-of-the-art alignment methods in handling very small shuffled reads containing multiple mutations 21 . Moreover, we combine them with substitutional tolerant Markov models (Supplementary Note 1), which are particularly useful to handle the specific characteristics of aDNA, mainly the large amount of substitutions.…”

Section: Methodsmentioning

confidence: 99%

FALCON-meta: a method to infer metagenomic composition of ancient DNA

Pratas

Pinho

Silva

et al. 2018

Preprint

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The general approaches to detect and quantify metagenomic sample composition are based on the alignment of the reads, according to an existing database containing reference microbial sequences. However, without proper parameterization, these methods are not suitable for ancient DNA. Quantifying somewhat dissimilar sequences by alignment methods is problematic, due to the need of fine-tuned thresholds, considering relaxed edit distances and the consequent increase of computational cost. Additionally, the choice of the thresholds poses the problem of how to quantify similarity without producing overestimated measures. We propose FALCON-meta, a compression-based method to infer metagenomic composition of next-generation sequencing samples. This unsupervised alignment-free method runs efficiently on FASTQ samples. FALCON-meta quickly learns how to give importance to the models that cooperate to predict similarity, incorporating parallelism and flexibility for multiple hardware characteristics. It shows substantial identification capabilities in ancient DNA without overestimation. In one of the examples, we found and authenticated an ancient Pseudomonas bacteria in a Mammoth mitogenome.FALCON-meta can be accessed at https://github.com/pratas/falcon.

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An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

Cited by 31 publications

References 62 publications

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

A Survey on Data Compression Methods for Biological Sequences

FALCON-meta: a method to infer metagenomic composition of ancient DNA

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