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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Detalles Bibliográficos
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
Descripción
Sumario: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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