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The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
We developed a pair of databases that support two important tasks: annotation of anonymous RNA transcripts and discovery of novel non-coding RNAs. The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686472/ https://www.ncbi.nlm.nih.gov/pubmed/18948287 http://dx.doi.org/10.1093/nar/gkn805 |
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author | Mituyama, Toutai Yamada, Kouichirou Hattori, Emi Okida, Hiroaki Ono, Yukiteru Terai, Goro Yoshizawa, Aya Komori, Takashi Asai, Kiyoshi |
author_facet | Mituyama, Toutai Yamada, Kouichirou Hattori, Emi Okida, Hiroaki Ono, Yukiteru Terai, Goro Yoshizawa, Aya Komori, Takashi Asai, Kiyoshi |
author_sort | Mituyama, Toutai |
collection | PubMed |
description | We developed a pair of databases that support two important tasks: annotation of anonymous RNA transcripts and discovery of novel non-coding RNAs. The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database (fRNAdb) and the latest version of the UCSC GenomeBrowser for Functional RNA. The former is a sequence database equipped with a powerful search function and hosts a large collection of known/predicted non-coding RNA sequences acquired from existing databases as well as novel/predicted sequences reported by researchers of the Functional RNA Project. The latter is a UCSC Genome Browser mirror with large additional custom tracks specifically associated with non-coding elements. It also includes several functional enhancements such as a presentation of a common secondary structure prediction at any given genomic window ⩽500 bp. Our GenomeBrowser supports user authentication and user-specific tracks. The current version of the fRNAdb is a complete rewrite of the former version, hosting a larger number of sequences and with a much friendlier interface. The current version of UCSC GenomeBrowser for Functional RNA features a larger number of tracks and richer features than the former version. The databases are available at http://www.ncrna.org/. |
format | Text |
id | pubmed-2686472 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-26864722009-05-26 The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs Mituyama, Toutai Yamada, Kouichirou Hattori, Emi Okida, Hiroaki Ono, Yukiteru Terai, Goro Yoshizawa, Aya Komori, Takashi Asai, Kiyoshi Nucleic Acids Res Articles We developed a pair of databases that support two important tasks: annotation of anonymous RNA transcripts and discovery of novel non-coding RNAs. The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database (fRNAdb) and the latest version of the UCSC GenomeBrowser for Functional RNA. The former is a sequence database equipped with a powerful search function and hosts a large collection of known/predicted non-coding RNA sequences acquired from existing databases as well as novel/predicted sequences reported by researchers of the Functional RNA Project. The latter is a UCSC Genome Browser mirror with large additional custom tracks specifically associated with non-coding elements. It also includes several functional enhancements such as a presentation of a common secondary structure prediction at any given genomic window ⩽500 bp. Our GenomeBrowser supports user authentication and user-specific tracks. The current version of the fRNAdb is a complete rewrite of the former version, hosting a larger number of sequences and with a much friendlier interface. The current version of UCSC GenomeBrowser for Functional RNA features a larger number of tracks and richer features than the former version. The databases are available at http://www.ncrna.org/. Oxford University Press 2009-01 2008-10-23 /pmc/articles/PMC2686472/ /pubmed/18948287 http://dx.doi.org/10.1093/nar/gkn805 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Mituyama, Toutai Yamada, Kouichirou Hattori, Emi Okida, Hiroaki Ono, Yukiteru Terai, Goro Yoshizawa, Aya Komori, Takashi Asai, Kiyoshi The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs |
title | The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs |
title_full | The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs |
title_fullStr | The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs |
title_full_unstemmed | The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs |
title_short | The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs |
title_sort | functional rna database 3.0: databases to support mining and annotation of functional rnas |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686472/ https://www.ncbi.nlm.nih.gov/pubmed/18948287 http://dx.doi.org/10.1093/nar/gkn805 |
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