Bioinformatics Bootcamp – Zebrafish Special Edition

A deep-dive into the many cool (and free) resources available to zebrafish researchers!

Disclaimer: This is not a comprehensive list but a list of useful websites that are free (or have free versions that are useful)

Featured Resources

• “The Mothership” – ZFIN (https://zfin.org/): Contains vital resources such as The Zebrafish Book, Thisse’s expression data & curated publications.

• “The Central Hub of Model Organism Databases” – Alliance of Genome Resources (https://www.alliancegenome.org/): The future of MODs.

• “Disease Modeling on Steroids” – MARRVEL (https://marrvel.org/ ): Super powerful resource including links to OMIM & ClinVar.

• “Ol’ Reliable Genome Browsing” – Ensembl (https://www.ensembl.org/Danio_rerio/Info/Index): Contains current & past genome assemblies in a easy(-ish) format. BLAST/BLAT is a powerful tool for queries.

• “Simplified Genome Browsing Software” – Integrative Genomics Viewer (https://igv.org/): Better as a desktop app. Lovely interface.

• “Genome Browsing With Bells and Whistles” – UCSC Genome Browser (https://genome.ucsc.edu/): Contains custom tracks such as ‘DANIO-CODE’ & ‘ZebrafishGenomics’ with super helpful CRISPR/Cas9 guide predictions via CRISPRscan.

• “One Repository to Rule Them All” – GEO DataSets (https://www.ncbi.nlm.nih.gov/gds): Shared resource for the life sciences & beyond.

• “The Exclusive Fishy Repository” – DANIO-CODE (https://danio-code.zfin.org/): Contains multiple stages across lifespan.

• “Work-(sea)horse of Bioinformatics” – DAVID (https://davidbioinformatics.nih.gov/): A beast of a website. A free alternative to Ingenuity Pathway Analysis.

• “The Controversial (sgRNA Predictions)” – CHOPCHOP (https://chopchop.cbu.uib.no/): Fantastic for selecting guides for generating F0 crispants and CRISPR knock-ins.
  

• “All Hail the UMAP!” – Daniocell (https://daniocell.nichd.nih.gov/): Turning into the gold-standard for zebrafish transcriptomics during early development.

• “Into the Multi-Ome” – Zebrahub (https://zebrahub.sf.czbiohub.org/): The future is here! Dynamic repository of development. And you must check out the videos!
  

• “Never-ending Search for Antibodies” – CiteAb (https://www.citeab.com/): If a zebrafish antibody does exist, it exists here.

• “Regeneration Rules!” – ZF REG DATABASE (http://zfregeneration.org/ ): See if your gene-of-interest has a role in regeneration across tissues.

• “Missed Connection” – STRING (https://string-db.org/ ): Finds the common link (e.g. expression data or literature reference) between your gene-of-interest & other potential hits in your datasets.

• “Trusted Resource for Craniofacial Researchers” – FaceBase (https://facebase.org/): Comparative dataset of musculoskeletal tissues across species.

Other useful websites and tools:

Protein Structure

• AlphaFold (https://alphafold.ebi.ac.uk/)

• UniProt (https://www.uniprot.org/)

Genomics

• BLASTn & BLASTp (https://blast.ncbi.nlm.nih.gov/Blast.cgi?)

• DIOPT Ortholog Finder (https://www.flyrnai.org/diopt)

• Expasy Translate Tool (https://web.expasy.org/translate/)

• SnapGene Viewer Software (https://www.snapgene.com/snapgene-viewer)

• Benchling (https://benchling.com/editor)

CRISPR Tools

• CRISPRscan (https://www.crisprscan.org/)
• IDT CRISPR-Cas9 guide RNA design checker (https://eu.idtdna.com/site/order/designtool/index/CRISPR_SEQUENCE)

MicroRNAs

• The Fish microRNA database (https://fishmirna.org/)
  
• TargetScanFish (https://www.targetscan.org/fish_62/)

Primer Design

• Primer-BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast/)

• Primer3Plus (https://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi)

Antibody Design

• AbDesigner (https://esbl.nhlbi.nih.gov/AbDesigner/)

Science Tools

• GraphPad Molarity Calculator (https://www.graphpad.com/quickcalcs/Molarityform.cfm)

Figure-making/Vector graphics

• Inkscape https://inkscape.org/

• BioArt Source: https://bioart.niaid.nih.gov/

• Bioicons: https://bioicons.com/

3D Models

• Thingiverse (https://www.thingiverse.com/)

Link to LinkedIn post: https://www.linkedin.com/posts/kevin-thiessen-ph-d-7470b8317_zebrafish-activity-7329457108599365632-GD2Q?utm_source=share&utm_medium=member_desktop&rcm=ACoAAFBIZScB1XZ47vLDomfVottzYLyczPZx56k

Link to Zebrafish Rock! website: https://linktr.ee/zebrafishrock

Credit preview image to illustrator Daryl Leja at NHGRI.

Links active as of 19th of May, 2025.

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