a comparative evaluation of sequence classification programs比较序列分类的评估程序.pdfVIP

Bazinet and Cummings BMC Bioinformatics 2012, 13:92 /1471-2105/13/92 RESEARCH ARTICLE Open Access A comparative evaluation of sequence classification programs * Adam L Bazinet and Michael P Cummings Abstract Background: A 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. Results: We 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. Conclusions: We 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. Background [1], Pfam [2]). On the basis of such comparisons, one A fundamental problem in modern genomics is to taxo- may be able to say with