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Protocols

ITSoneDB specifications

Information


Unique identifier OMICS_22091
Name ITSoneDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Graziano Pesole

Publication for ITSoneDB

ITSoneDB citations

 (4)
library_books

New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida)

2017
Ecol Evol
PMCID: 5723599
PMID: 29238565
DOI: 10.1002/ece3.3212

[…] & Rygiewicz, ; Nilsson, Kristiansson, Ryberg, Hallenberg, & Larsson, ; Rampersad, ). ITS1 is used in molecular identification of fungi in the publicly available databases UNITE (Koljalg et al., ) and ITSoneDB (Fosso et al., ), but the annotation and analyses of ITS1 of other taxonomic groups may be challenging. Because annotation is commonly performed by directly comparing new amplicons with those […]

library_books

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

2017
Front Microbiol
PMCID: 5622200
PMID: 28993761
DOI: 10.3389/fmicb.2017.01657

[…] through sequence similarity (BLAST) searches against public databases such as NCBI's GenBank (Benson et al., ) or more specific ITS databases, such as UNITE (Kõljalg et al., ; Abarenkov et al., ) or ITSoneDB (Santamaria et al., ). The quality of these databases, however, strongly depends on the quantity of relevant content and scientific rigor of contributors, and the more comprehensive the datab […]

library_books

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

2016
mSystems
PMCID: 5080400
PMID: 27822552
DOI: 10.1128/mSystems.00052-16

[…] with a BLAST search () against SILVA SSURef database release 1 (). ITS gene sequencing data were processed with a slightly modified pipeline. Taxonomy was assigned by using a BLAST search against the ITSoneDB database (). Raw reads from whole-metagenome shotgun sequencing were filtered on the basis of quality and quantity and trimmed to 200 bp with a combination of Picardtools (https://github.com/ […]

call_split

Sequencing Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

2013
PLoS One
PMCID: 3716650
PMID: 23894461
DOI: 10.1371/journal.pone.0069371
call_split See protocol

[…] ITS sequences are known to harbour long homopolymer runs. Trimmed fasta sequences were assessed by BLAST analysis against the SILVA database (version 100) for 16S reads . The ITS-1 specific database, ITSoneDB, was used to BLAST all ITS sequences . BLAST outputs were parsed using MEGAN with a bit-score of 86 was employed for 16S ribosomal sequence data, and a bit-score of 35 was used for ITS seque […]


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ITSoneDB institution(s)
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy; Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari, Italy; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari ‘A. Moro’, Bari, Italy
ITSoneDB funding source(s)
Supported by the Italian Ministry for Education, University and Research; LifeWatch, ELIXIR-IIB, ‘PON Ricerca e Competitivita 2007–2013’ Program; ReCaS (Azione I-Interventi di rafforzamento strutturale, PONa3 00052, Avviso 254/Ric); PRISMA (Asse II-Sostegno all’innovazione, PON04a2 A); European Commission (ELIXIREXCELERATE HORIZON 2020, EMBRIC HORIZON 2020).

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