TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences

Alexander Tuzhikov, Alexander Panchin, Valery I Shestopalov

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. Te routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. Te taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classifications; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina.

Original languageEnglish
Pages (from-to)78-84
Number of pages7
JournalBioTechniques
Volume56
Issue number2
DOIs
StatePublished - Feb 1 2014

Fingerprint

Nucleotides
16S Ribosomal RNA
Databases
Classifiers
Genes
DNA sequences
Microbiota
rRNA Genes
Base Pairing

Keywords

  • Bioinformatics
  • Metagenome
  • Microbiome
  • Next-generation sequencing
  • Software
  • Taxonomic classification

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biotechnology

Cite this

TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences. / Tuzhikov, Alexander; Panchin, Alexander; Shestopalov, Valery I.

In: BioTechniques, Vol. 56, No. 2, 01.02.2014, p. 78-84.

Research output: Contribution to journalArticle

Tuzhikov, Alexander ; Panchin, Alexander ; Shestopalov, Valery I. / TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences. In: BioTechniques. 2014 ; Vol. 56, No. 2. pp. 78-84.
@article{c3c0a07ec5bf4167ab2290f05278cfdb,
title = "TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences",
abstract = "Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. Te routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. Te taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classifications; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina.",
keywords = "Bioinformatics, Metagenome, Microbiome, Next-generation sequencing, Software, Taxonomic classification",
author = "Alexander Tuzhikov and Alexander Panchin and Shestopalov, {Valery I}",
year = "2014",
month = "2",
day = "1",
doi = "10.2144/000114135",
language = "English",
volume = "56",
pages = "78--84",
journal = "BioTechniques",
issn = "0736-6205",
publisher = "Eaton Publishing Company",
number = "2",

}

TY - JOUR

T1 - TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences

AU - Tuzhikov, Alexander

AU - Panchin, Alexander

AU - Shestopalov, Valery I

PY - 2014/2/1

Y1 - 2014/2/1

N2 - Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. Te routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. Te taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classifications; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina.

AB - Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. Te routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. Te taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classifications; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina.

KW - Bioinformatics

KW - Metagenome

KW - Microbiome

KW - Next-generation sequencing

KW - Software

KW - Taxonomic classification

UR - http://www.scopus.com/inward/record.url?scp=84893583895&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84893583895&partnerID=8YFLogxK

U2 - 10.2144/000114135

DO - 10.2144/000114135

M3 - Article

VL - 56

SP - 78

EP - 84

JO - BioTechniques

JF - BioTechniques

SN - 0736-6205

IS - 2

ER -