FishDB: an integrated functional genomics database for fishes.

BMC Genomics
Liandong YangShunping He

Abstract

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. 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. This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules.

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

BioMart
TBLASTN
piRBase
Trinity
GCGD
Blast
BLASTN
Ensembl
NONCODE
JBrowse

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