ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences
| Autor: | Bachir Balech, Bruno Fosso, Giorgio De Caro, Sabino Liuni, Flavio Licciulli, Giorgio Grillo, Monica Santamaria, Graziano Pesole, Ilaria Larini |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
European Nucleotide Archive 5.8S ribosomal RNA Computational biology Biology 18S ribosomal RNA DNA metabarcoding Database 03 medical and health sciences User-Computer Interface 28S ribosomal RNA DNA Ribosomal Spacer Genetics Database Issue Animals DNA Barcoding Taxonomic Humans Internal transcribed spacer Internet 030102 biochemistry & molecular biology Eukaryotic communities Eukaryota Molecular Sequence Annotation Spacer DNA Ribosomal RNA 030104 developmental biology Metagenomics RNA Ribosomal Multigene Family Databases Nucleic Acid |
| Zdroj: | Nucleic Acids Research Nucleic acids research (Online) (2017): D127–D132. doi:10.1093/nar/gkx855 info:cnr-pdr/source/autori:Santamaria M., Fosso B., Licciulli F., Balech B., Larini I., Grillo G., De Caro G., Liuni S., Pesole G./titolo:ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences./doi:10.1093%2Fnar%2Fgkx855/rivista:Nucleic acids research (Online)/anno:2017/pagina_da:D127/pagina_a:D132/intervallo_pagine:D127–D132/volume |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkx855 |
| Popis: | A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|