A comparative evaluation of sequence classification programs

BMC Bioinformatics

Research Article

Adam L Bazinet¹  Michael P Cummings¹ 

[1] Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, 20874, College Park, MD, USA;

关键词: Marker Gene;    Query Sequence;    Genus Rank;    Bloom Filter;    Assignment Accuracy;   

DOI  :  10.1186/1471-2105-13-92

 received in 2012-02-22, accepted in 2012-04-20,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundA fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics). Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis.ResultsWe divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known.ConclusionsWe found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

【 授权许可】

CC BY   
© Bazinet and Cummings; licensee BioMed Central Ltd. 2012