Detail publikace

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

SEDLÁŘ, K. KUPKOVÁ, K. PROVAZNÍK, I.

Originální název

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments. On the other hand, the output of whole metagenomic shotgun sequencing is mixture of short DNA fragments belonging to various genomes, therefore this approach requires more sophisticated computational algorithms for clustering of related sequences, commonly referred to as sequence binning. There are currently two types of binning methods: taxonomy dependent and taxonomy independent. The first type classifies the DNA fragments by performing a standard homology inference against a reference database, while the latter performs the reference-free binning by applying clustering techniques on features extracted from the sequences. In this review, we describe the strategies within the second approach. Although these strategies do not require prior knowledge, they have higher demands on the length of sequences. Besides their basic principle, an overview of particular methods and tools is provided. Furthermore, the review covers the utilization of the methods in context with the length of sequences and discusses the needs for metagenomic data preprocessing in form of initial assembly prior to binning.

Klíčová slova

Metagenomics; Taxonomy independent; Sequence binning; Genomic signature; Abundance; Visualization

Autoři

SEDLÁŘ, K.; KUPKOVÁ, K.; PROVAZNÍK, I.

Vydáno

5. 12. 2016

Nakladatel

Elsevier

ISSN

2001-0370

Periodikum

Computational and Structural Biotechnology Journal

Ročník

15

Číslo

1

Stát

Švédské království

Strany od

48

Strany do

55

Strany počet

8

URL

http://www.sciencedirect.com/science/article/pii/S2001037016300678

Plný text v Digitální knihovně

http://hdl.handle.net/11012/69196

BibTex

@article{BUT130296,
  author="Karel {Sedlář} and Kristýna {Kupková} and Valentine {Provazník}",
  title="Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics",
  journal="Computational and Structural Biotechnology Journal",
  year="2016",
  volume="15",
  number="1",
  pages="48--55",
  doi="10.1016/j.csbj.2016.11.005",
  issn="2001-0370",
  url="http://www.sciencedirect.com/science/article/pii/S2001037016300678"
}