FAQs - General
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FAQs - General

Where do I find the GFF file for download?

The Genomics directory on the FTP site has the GFF3 file.

You can find this by going to the Downloads drop down, 

then select Browse Echinobase FTP.

Then select Genomics and the species of interest.

The species subdirectories have the GFF3 file and the transcripts, CDS and proteins FASTA files.

Here is a tutorial video describing data available at Echinobase. 


How do we go about naming genes?

The naming and updating of names is an ongoing process.

There is an overview in this tutorial video.

The FAQs - Gene Names and IDs is dedicated to these questions.


Is there a brief video to highlight features of Echinobase?

Yes, here is a short video with an overview of Echinobase content.


Where is the old EchinoBase?

The previous EchinoBase can be found here.

This site will not be maintained indefinitely.

On July 13, 2020 Echinobase switched to a new server featuring a new S. purpuratus v5.0 genome, updated gene pages, orthology, and more! This older version of Echinobase is currently supported as a legacy website, but will eventually be retired.

We encourage you to start using the new server as soon as possible so that your work will not be interrupted when this legacy site is shut down.


How do we get started with CRISPR experiments?

Echinobase has a wiki page where the published studies of gene editing in echinoderms are reviewed, the methods summarized and gRNAs listed. 

The gRNAs are now available on the Gene Pages.

Link to the page: CRISPR/Cas in Echinoderms 


Who can help us if we have further questions?

The Echinobase team is here to answer questions.

If you are looking for an individual that you know has expertise, their contact information is available from the Community Search.

If you are trying to find who has the knowledge then enter your query terms into the Literature Search to see who has published on the subject. 



Last Updated: 2024-01-19