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BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori
BACKGROUND: Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rar...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5022206/ https://www.ncbi.nlm.nih.gov/pubmed/27623959 http://dx.doi.org/10.1186/s12859-016-1251-y |
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author | Zhou, Qiu-Zhong Zhang, Bindan Yu, Quan-You Zhang, Ze |
author_facet | Zhou, Qiu-Zhong Zhang, Bindan Yu, Quan-You Zhang, Ze |
author_sort | Zhou, Qiu-Zhong |
collection | PubMed |
description | BACKGROUND: Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). DESCRIPTION: In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. CONCLUSIONS: We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1251-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5022206 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-50222062016-09-20 BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori Zhou, Qiu-Zhong Zhang, Bindan Yu, Quan-You Zhang, Ze BMC Bioinformatics Database BACKGROUND: Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). DESCRIPTION: In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. CONCLUSIONS: We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1251-y) contains supplementary material, which is available to authorized users. BioMed Central 2016-09-13 /pmc/articles/PMC5022206/ /pubmed/27623959 http://dx.doi.org/10.1186/s12859-016-1251-y Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Database Zhou, Qiu-Zhong Zhang, Bindan Yu, Quan-You Zhang, Ze BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori |
title | BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori |
title_full | BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori |
title_fullStr | BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori |
title_full_unstemmed | BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori |
title_short | BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori |
title_sort | bmncrnadb: a comprehensive database of non-coding rnas in the silkworm, bombyx mori |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5022206/ https://www.ncbi.nlm.nih.gov/pubmed/27623959 http://dx.doi.org/10.1186/s12859-016-1251-y |
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