Jan 27, 2016

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken)

Journal of Microbiological Methods
Fabiola Valenzuela-GonzálezFrancisco Vargas-Albores

Abstract

Ultrafast-metagenomic sequence classification using exact alignments (Kraken) is a novel approach to classify 16S rDNA sequences. The classifier is based on mapping short sequences to the lowest ancestor and performing alignments to form subtrees with specific weights in each taxon node. This study aimed to evaluate the classification performance of Kraken with long 16S rDNA random environmental sequences produced by cloning and then Sanger sequenced. A total of 480 clones were isolated and expanded, and 264 of these clones formed contigs (1352 ± 153 bp). The same sequences were analyzed using the Ribosomal Database Project (RDP) classifier. Deeper classification performance was achieved by Kraken than by the RDP: 73% of the contigs were classified up to the species or variety levels, whereas 67% of these contigs were classified no further than the genus level by the RDP. The results also demonstrated that unassembled sequences analyzed by Kraken provide similar or inclusively deeper information. Moreover, sequences that did not form contigs, which are usually discarded by other programs, provided meaningful information when analyzed by Kraken. Finally, it appears that the assembly step for Sanger sequences can be eliminated wh...Continue Reading

  • References13
  • Citations3

Mentioned in this Paper

Study
Classification
Alkalescens-Dispar Group
DNA, Ribosomal
Nucleic Acid Sequencing
Evaluation
Metagenomics
Computer Programs and Programming
Objective (Goal)
Clone

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