Complexity Profiles of DNA Sequences Using Finite-Context Models

Pinho, Armando J.; Pratas, Diogo; Garcia, Sara P.

doi:10.1007/978-3-642-25364-5_8

Cited by 4 publications

(4 citation statements)

References 29 publications

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“…Moreover, there is also the possibility to use the reverse complement repeats, where they can also be exact or approximate copies. An example can be seen in Figure 3 , with information profiles assessment [ 35 , 36 ], where the zones of low complexity are related with similarity, and hence, exact or approximate repetitions seen in other parts of the sequence, as in the first plot (real DNA FASTQ sequence). The second plot shows a simulated sequence with absence of repeats, and hence, the zones of low complexity are also absent.…”

Section: Resultsmentioning

confidence: 99%

XS: a FASTQ read simulator

2014

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BackgroundThe emerging next-generation sequencing (NGS) is bringing, besides the natural huge amounts of data, an avalanche of new specialized tools (for analysis, compression, alignment, among others) and large public and private network infrastructures. Therefore, a direct necessity of specific simulation tools for testing and benchmarking is rising, such as a flexible and portable FASTQ read simulator, without the need of a reference sequence, yet correctly prepared for producing approximately the same characteristics as real data.FindingsWe present XS, a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores).ConclusionsXS provides an efficient and convenient method for fast simulation of FASTQ files, such as those from Ion Torrent (currently uncovered by other simulators), Roche-454, Illumina and ABI-SOLiD sequencing machines. This tool is publicly available at http://bioinformatics.ua.pt/software/xs/.

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Section: Resultsmentioning

confidence: 99%

XS: a FASTQ read simulator

2014

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“…The construction of these profiles follows a pipeline formed of many transformations (e.g. reversing, segmenting, inverting) as well as the use of specific low-pass filters after data compression applications [11]. Fig.…”

Section: Bi-directional Complexity Profilesmentioning

confidence: 99%

GTO: A toolkit to unify pipelines in genomic and proteomic research

et al. 2020

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“…The construction of these profiles follow a pipeline constituted by many transformations (e.g. reversing, segmenting, inverting) and well as the use of specific low-pass filters after data compression applications [5]. Figure 1 depicts the complexity profiles of four human Herpesvirus whole genomes using the same scale, where redundant regions are highlighted with blue (below a Bps of one).…”

Section: Validationmentioning

confidence: 99%

GTO: a toolkit to unify pipelines in genomic and proteomic research

Almeida

Pinho

Oliveira

et al. 2020

Preprint

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Next-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools are needed, given the dynamics and specificities of the field. We present GTO, a comprehensive toolkit designed to unify pipelines in genomic and proteomic research, which combines specialised tools for analysis, simulation, compression, development, visualisation, and transformation of the data. This toolkit combines novel tools with a modular architecture, being an excellent platform for experimental scientists, as well as a useful resource for teaching bioinformatics inquiry to students in life sciences.

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Complexity Profiles of DNA Sequences Using Finite-Context Models

Cited by 4 publications

References 29 publications

XS: a FASTQ read simulator

XS: a FASTQ read simulator

GTO: A toolkit to unify pipelines in genomic and proteomic research

GTO: a toolkit to unify pipelines in genomic and proteomic research

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