The Effect of Sequence Error and Partial Training Data on BLAST Accuracy

Metagenomics is the study of environmental samples. Because few tools exist for metagenomic analysis, a natural step has been to utilize the popular homology tool, BLAST, to search for sequence similarity between DNA reads and an administered database. Most biologists use this method today without knowing BLAST’s accuracy, especially when a particular taxonomic class is under-represented in the database. The aim of this paper is to benchmark the performance of BLAST for taxonomic classification of metagenomic datasets in a supervised setting, meaning that the database contains microbes of the same class as the ‘unknown’ query DNA reads. We examine well- and under-represented genera and phyla in order to study their effect on the accuracy of BLAST. We investigate the degradation in BLAST accuracy when genome coverage is reduced in the training database as well as the performance when errors are introduced into the query DNA reads. We conclude that on fine-resolution classes, such as genera, the accuracy of BLAST does not degrade very much with under-representation, but in a highly variant class, such as phyla, performance degrades significantly when whole genomes are used in the training database. BLAST accuracy at the genus level is affected greater than phyla when coverage in the training database is reduced or when 1% sequence error is introduced into the query DNA reads. Our analysis includes five-fold cross validation to substantiate our findings.