Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Mituyama, Toutai, Yamada, Kouichirou, Hattori, Emi, Okida, Hiroaki, Ono, Yukiteru, Terai, Goro, Yoshizawa, Aya, Komori, Takashi, Asai, Kiyoshi
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
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
_version_ 1782167415393615872
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
work_keys_str_mv AT mituyamatoutai thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT yamadakouichirou thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT hattoriemi thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT okidahiroaki thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT onoyukiteru thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT teraigoro thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT yoshizawaaya thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT komoritakashi thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT asaikiyoshi thefunctionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT mituyamatoutai functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT yamadakouichirou functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT hattoriemi functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT okidahiroaki functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT onoyukiteru functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT teraigoro functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT yoshizawaaya functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT komoritakashi functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas
AT asaikiyoshi functionalrnadatabase30databasestosupportminingandannotationoffunctionalrnas