Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction

Tran, Ngoc Hieu; Chen, Xin

doi:10.1186/1756-0500-7-320

Cited by 9 publications

(6 citation statements)

References 36 publications

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“…The set of 29 E . coli genome sequences was originally compiled by Yin and Jin [23] and has been used in the past by other groups to evaluate AF programs [24, 25, 89]. Finally, the set of 14 plant genomes is from Hatje et al [90].…”

Section: Methodsmentioning

confidence: 99%

Benchmarking of alignment-free sequence comparison methods

et al. 2019

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Background Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Results Here, we present a community resource ( http://afproject.org ) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. Conclusion The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions. Electronic supplementary material The online version of this article (10.1186/s13059-019-1755-7) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Benchmarking of alignment-free sequence comparison methods

et al. 2019

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“…The sequences of 25 whole mitochondrial genomes of fish species from the suborder Labroidei and the species tree were taken from Fischer et al [48]. The set of 29 E. coli genome sequences was originally compiled by Yin and Jin [21] and has been used in the past by other groups to evaluate AF programs [22,23,68]. Finally, the set of 14 plant genomes is from Hatje et al [69].…”

Section: Data Setsmentioning

confidence: 99%

Benchmarking of alignment-free sequence comparison methods

Zieleziński

Girgis

Bernard

et al. 2019

Preprint

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2 Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events.The interactive web service allows researchers to explore the performance of alignmentfree tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-theart tools, accelerating the development of new, more accurate AF solutions. BACKGROUNDComparative analysis of DNA and amino acid sequences is of fundamental importance in biological research, particularly in molecular biology and genomics. It is the first and key step in molecular evolutionary analysis, gene function and regulatory region prediction, sequence assembly, homology searching, molecular structure prediction, gene discovery and protein structure-function relationships analysis. Traditionally, sequence comparison was based on pairwise or multiple sequence alignment (MSA). Software tools for sequence alignment, such as BLAST [1] and CLUSTAL [2], are the most widely used bioinformatics methods.Although alignment-based approaches generally remain the references for sequence

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“…Because MSA is limited by the size of the genome, only the 29 mammalian mtDNA dataset is capable of using the tree from MSA as the benchmark tree. The benchmark tree for 29 Escherichia/Shigella is the tree studied by the research [28], [33] and 18 Drosophila genomes tree is from the phylogenetic tree database Open Tree of life [10], [34], [35]. In our implementation, we also used the USEARCH tool [36] to search for the alignment pair of any NGS short reads.…”

Section: Evaluation Metricmentioning

confidence: 99%

An Effective Parameter-free Comparison of NGS Short Reads for Phylogeny Reconstruction

Chotnithi

Lê

Takasu

2019

Journal of Information Processing

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With the growth of the amount of genomic data generated from high-throughput sequencing, nextgeneration sequencing (NGS) has become the mainstream format for genome sequence data. NGS presents new challenges for many applications for genome sequence analysis. In sequence comparison applications, traditional multiple-sequence alignment approaches do not provide a solution for analyzing NGS data because of the short-read assembly and computational resource problems. Thus, alignment-free methods are more suitable for NGS data comparisons. Most of the alignment-free methods are based on the k-mer algorithm. However, the characteristics of NGS data make such k-mer-based methods suboptimal because the k parameter is a crucial factor in distance measurement and for the construction of phylogenetic trees. We propose an effective parameter-free comparison of NGS short reads, with the aim of eliminating the dependency on the k parameters. We compared the proposed method with existing methods, and the results show that the proposed method can measure accurate distances for the dataset without requiring any parameter.

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Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction

Cited by 9 publications

References 36 publications

Benchmarking of alignment-free sequence comparison methods

Benchmarking of alignment-free sequence comparison methods

Benchmarking of alignment-free sequence comparison methods

An Effective Parameter-free Comparison of NGS Short Reads for Phylogeny Reconstruction

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