Next generation sequencing reads comparison with an alignment-free distance
Identifieur interne : 001B32 ( Main/Exploration ); précédent : 001B31; suivant : 001B33Next generation sequencing reads comparison with an alignment-free distance
Auteurs : Emanuel Weitschek [Italie] ; Daniele Santoni [Italie] ; Giulia Fiscon [Italie] ; Maria Cristina De Cola [Italie] ; Paola Bertolazzi [Italie] ; Giovanni Felici [Italie]Source :
- BMC Research Notes [ 1756-0500 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- Algorithms, DNA, Bacterial (chemistry), DNA, Bacterial (genetics), DNA, Fungal (chemistry), DNA, Fungal (genetics), Escherichia coli (genetics), High-Throughput Nucleotide Sequencing, Humans, Saccharomyces cerevisiae (genetics), Sequence Alignment (methods), Sequence Alignment (statistics & numerical data), Sequence Analysis, DNA (methods), Sequence Analysis, DNA (statistics & numerical data).
- MESH :
- chemical , chemistry : DNA, Bacterial, DNA, Fungal.
- chemical , genetics : DNA, Bacterial, DNA, Fungal.
- genetics : Escherichia coli, Saccharomyces cerevisiae.
- methods : Sequence Alignment, Sequence Analysis, DNA.
- statistics & numerical data : Sequence Alignment, Sequence Analysis, DNA.
- Algorithms, High-Throughput Nucleotide Sequencing, Humans.
Abstract
Next Generation Sequencing (NGS) machines extract from a biological sample a large number of short DNA fragments (
We propose a method to evaluate the similarity between reads. This method does not rely on the alignment of the reads and it is based on the distance between the frequencies of their substrings of fixed dimensions (
We exhibit experimental evidence that the proposed alignment-free distance is a potentially useful read-to-read distance measure and performs better than the more time consuming distances based on alignment.
Alignment-free distances may be used effectively for reads comparison, and may provide a significant speed-up in several processes based on NGS sequencing (e.g., DNA assembly, reads classification).
The online version of this article (doi:10.1186/1756-0500-7-869) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1756-0500-7-869
PubMed: 25465386
PubMed Central: 4265526
Affiliations:
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Le document en format XML
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<term>DNA, Bacterial (chemistry)</term>
<term>DNA, Bacterial (genetics)</term>
<term>DNA, Fungal (chemistry)</term>
<term>DNA, Fungal (genetics)</term>
<term>Escherichia coli (genetics)</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Saccharomyces cerevisiae (genetics)</term>
<term>Sequence Alignment (methods)</term>
<term>Sequence Alignment (statistics & numerical data)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Sequence Analysis, DNA (statistics & numerical data)</term>
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<term>Algorithmes</term>
<term>Alignement de séquences ()</term>
<term>Analyse de séquence d'ADN ()</term>
<term>Escherichia coli (génétique)</term>
<term>Humains</term>
<term>Saccharomyces cerevisiae (génétique)</term>
<term>Séquençage nucléotidique à haut débit</term>
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<term>DNA, Fungal</term>
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<term>DNA, Fungal</term>
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<term>Saccharomyces cerevisiae</term>
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<term>ADN fongique</term>
<term>Escherichia coli</term>
<term>Saccharomyces cerevisiae</term>
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<term>Sequence Analysis, DNA</term>
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<term>Sequence Analysis, DNA</term>
</keywords>
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<term>High-Throughput Nucleotide Sequencing</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Next Generation Sequencing (NGS) machines extract from a biological sample a large number of short DNA fragments (<italic>reads</italic>
). These reads are then used for several applications, e.g., sequence reconstruction, DNA assembly, gene expression profiling, mutation analysis.</p>
</sec>
<sec><title>Methods</title>
<p>We propose a method to evaluate the similarity between reads. This method does not rely on the alignment of the reads and it is based on the distance between the frequencies of their substrings of fixed dimensions (<italic>k</italic>
-mers). We compare this alignment-free distance with the similarity measures derived from two alignment methods: Needleman-Wunsch and Blast. The comparison is based on a simple assumption: the most correct distance is obtained by knowing in advance the reference sequence. Therefore, we first align the reads on the original DNA sequence, compute the overlap between the aligned reads, and use this overlap as an ideal distance. We then verify how the alignment-free and the alignment-based distances reproduce this ideal distance. The ability of correctly reproducing the ideal distance is evaluated over samples of read pairs from <italic>Saccharomyces cerevisiae</italic>
, <italic>Escherichia coli</italic>
, and <italic>Homo sapiens</italic>
. The comparison is based on the correctness of threshold predictors cross-validated over different samples.</p>
</sec>
<sec><title>Results</title>
<p>We exhibit experimental evidence that the proposed alignment-free distance is a potentially useful read-to-read distance measure and performs better than the more time consuming distances based on alignment.</p>
</sec>
<sec><title>Conclusions</title>
<p>Alignment-free distances may be used effectively for reads comparison, and may provide a significant speed-up in several processes based on NGS sequencing (e.g., DNA assembly, reads classification).</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/1756-0500-7-869) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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</back>
</TEI>
<affiliations><list><country><li>Italie</li>
</country>
<region><li>Latium</li>
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<settlement><li>Rome</li>
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<tree><country name="Italie"><region name="Latium"><name sortKey="Weitschek, Emanuel" sort="Weitschek, Emanuel" uniqKey="Weitschek E" first="Emanuel" last="Weitschek">Emanuel Weitschek</name>
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<name sortKey="De Cola, Maria Cristina" sort="De Cola, Maria Cristina" uniqKey="De Cola M" first="Maria Cristina" last="De Cola">Maria Cristina De Cola</name>
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<name sortKey="Weitschek, Emanuel" sort="Weitschek, Emanuel" uniqKey="Weitschek E" first="Emanuel" last="Weitschek">Emanuel Weitschek</name>
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