FishDB: an integrated functional genomics database for fishes

BACKGROUND: Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data. RESULTS: Here we present FishDB, the first database for fish multi-level omic...

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Autores principales: Yang, Liandong, Xu, Zetan, Zeng, Honghui, Sun, Ning, Wu, Baosheng, Wang, Cheng, Bo, Jing, Li, Lin, Dong, Yang, He, Shunping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Database
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670658/
https://www.ncbi.nlm.nih.gov/pubmed/33203359
http://dx.doi.org/10.1186/s12864-020-07159-9
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author Yang, Liandong
Xu, Zetan
Zeng, Honghui
Sun, Ning
Wu, Baosheng
Wang, Cheng
Bo, Jing
Li, Lin
Dong, Yang
He, Shunping
author_facet Yang, Liandong
Xu, Zetan
Zeng, Honghui
Sun, Ning
Wu, Baosheng
Wang, Cheng
Bo, Jing
Li, Lin
Dong, Yang
He, Shunping
author_sort Yang, Liandong
collection PubMed
description BACKGROUND: Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data. RESULTS: Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb.ihb.ac.cn. The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes. CONCLUSIONS: This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07159-9.
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spelling pubmed-76706582020-11-18 FishDB: an integrated functional genomics database for fishes Yang, Liandong Xu, Zetan Zeng, Honghui Sun, Ning Wu, Baosheng Wang, Cheng Bo, Jing Li, Lin Dong, Yang He, Shunping BMC Genomics Database BACKGROUND: Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data. RESULTS: Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb.ihb.ac.cn. The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes. CONCLUSIONS: This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07159-9. BioMed Central 2020-11-17 /pmc/articles/PMC7670658/ /pubmed/33203359 http://dx.doi.org/10.1186/s12864-020-07159-9 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.
spellingShingle Database
Yang, Liandong
Xu, Zetan
Zeng, Honghui
Sun, Ning
Wu, Baosheng
Wang, Cheng
Bo, Jing
Li, Lin
Dong, Yang
He, Shunping
FishDB: an integrated functional genomics database for fishes
title FishDB: an integrated functional genomics database for fishes
title_full FishDB: an integrated functional genomics database for fishes
title_fullStr FishDB: an integrated functional genomics database for fishes
title_full_unstemmed FishDB: an integrated functional genomics database for fishes
title_short FishDB: an integrated functional genomics database for fishes
title_sort fishdb: an integrated functional genomics database for fishes
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670658/
https://www.ncbi.nlm.nih.gov/pubmed/33203359
http://dx.doi.org/10.1186/s12864-020-07159-9
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