CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences
| Autor: | Natalie Vande Pol, Kristi Gdanetz, Gregory Bonito, Gian Maria Niccolò Benucci |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Computer science 030106 microbiology Computational biology lcsh:Computer applications to medicine. Medical informatics Biochemistry UPARSE mycobiome 03 medical and health sciences RDP Structural Biology Environmental Microbiology Taxonomic rank Microbiome Internal transcribed spacer DNA Fungal Molecular Biology Ribosomal DNA UNOISE lcsh:QH301-705.5 Methodology Article Applied Mathematics Fungi High-Throughput Nucleotide Sequencing Genomics Biological classification fungal microbiome Computer Science Applications 030104 developmental biology lcsh:Biology (General) Taxonomic resolution lcsh:R858-859.7 DNA Intergenic Taxonomy (biology) taxonomy classifiers Genome Fungal DNA microarray ITS Classifier (UML) Software Mycobiome SINTAX |
| Zdroj: | BMC Bioinformatics, Vol 18, Iss 1, Pp 1-9 (2017) BMC Bioinformatics |
| ISSN: | 1471-2105 |
| Popis: | Background One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent. Results Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SINTAX) handle ITS fungal sequence data. The classification power, defined as the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers. Classifiers were generally consistent (assignment of the same taxonomy to a given OTU) across datasets and ranks; a small number of OTUs were assigned unique classifications across programs. We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merges them into an improved consensus taxonomy. This tool also produces summary classification outputs that are useful for downstream analyses. Conclusions Our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power is realized by generating consensus taxonomy of available classifiers with CONSTAX. Electronic supplementary material The online version of this article (10.1186/s12859-017-1952-x) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|