In the search page, users can search gene / RNA by filling out a form.
These forms can be filled in optionally, and the database will return results that meet conditional conditions.
This is a gene case.
Search by bioproject
In the search page, users can search bioproject by filling out a form.
This forms can be filled in optionally, and the database will return results that meet conditional conditions.
This is a bioproject case.
Expression
In the expression page, users can click nodes in the folded tree to obtain information about all bioprojects, including description information, keywords, article information, sample list and descriptioninformation.
The users choose one or more samples, which can come from the same or multiple bioprojects, and then queries through symbol or manually insets gene ID /RNA ID. After running, visualization of expression profile will be carried out. The returned result is usually a dynamic interactive heat map.
When the specified sample or gene ID /RNA ID is one, a bar graph will be generated.
When users select zebrafish sample, the dynamic interactive line chart will also be provided to show the changes of gene/RNA over time.
If there is a co-expression relationship among the genes selected by users, a network diagram of these genes will also be generated.
Coding ability prediction
In the page of coding ability prediction, users can upload transcript sequences and get higher-accuracy results through a joint analysis strategy (Duan et al., 2020) based on CPAT (3.0.4) (Wang et al., 2013) and CPC2 (Kang et al., 2017). Sequences were flagged as mRNAs, lncRNAs, or transcripts with uncertain coding potential (TUCP).
Expression count
In the page of expression count, based on user-uploaded paired-end sequencing data in fastq.gz format, the expression count tool quantifies gene/transcript expression in user-specified species. The results include the gene raw count table generated by Verse and transcript-level expression tables generated by Salmon.
Neighbor
In the neighbor page, after entering the gene / RNA ID in FishGET, users can set the distance interval and select species freely, and then obtain the detailed information of all gene / RNA within the desired interval.
This is a gene case.
BLAST
Users can paste sequences or upload files to query FishGET based on sequence similarity.
General search options provide a parameter named db, which allows users to perform similarity searches for one or all species in FishGET.
Other parameters are set by default for users, and the output format is tabular with comment lines, which is our most recommended.
Download
In the download page, FishGET provides data downloads for each species.
Including gene/RNA table, GTF File, FASTA File of RNA, expression table of gene/RNA, and Co-expression table.
Among them, gene/RNA table is a summary table sorted by us, including species information, type information, attribute information, location information, NR/GO/KEGG information and other basic information.
Gene
RNA
