Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

AbundanceBin, Metagenomic Sequencing

  • Yuzhen YeEmail author
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_29-4

Definition

Binning is unsupervised clustering of metagenomic sequences into an unknown set of species.

AbundanceBin is a binning tool utilizing the different abundances of the species in a community.

Introduction

Binning is one of the challenging problems in the metagenomics field. It has two main applications. One application is for studying the structure of microbial communities. The other application is for improving the downstream analysis of metagenomic sequences, including metagenome assembly (which has shown to be extremely difficult), considering that assembling reads one bin at a time significantly reduces the complexity of the metagenome assembly problem.

Composition-based methods have been the main approaches to unsupervised classification of reads. The basis of these approaches is that the genome composition (G + C content, dinucleotide frequencies, and synonymous codon usage) vary among organisms and are generally characteristic of evolutionary lineages. Tools in this...

Keywords

Synonymous Codon Usage Metagenomic Sequence Lower Common Ancestor Metagenomic Dataset Lower Common Ancestor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Indiana University, School of Informatics and ComputingBloomingtonUSA