Table of Contents

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• Zebrafish Genome Browser at UCSC:

  A joint collaboration between UCSC and the Zebrafish Genome Initiative at Children's Hospital Boston provides several useful tracks of genome data, including:

• • Mapping & Sequencing: Position / Conigs / Scaffolds / RH Map / BAC End Pairs & Singles / Gap / GC Percent
  • Genes & Gene Prediction: RefSeq Genes / Ensembl Genes
  • mRNA & EST: ZF mRNAs & ESTs / spliced ESTs / WZ EST Clusters / nonZF mRNAs
  • Expression & Regulation: Affy ZF
  • Comparative Genomics: Fugu Chain & Net / Human Proteins / HG Blast
  • Variation & Repeats: RepeatMasker / SimpleRepeats

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• Zebrafish Genome Resources at NCBI:

  This page provides information about genomic resources available from NCBI and the zebrafish research community, including sequence, mapping, clone information, and NCBI's independent gene annotation.

• SNPFisher : Variant Report Compiler:

  Variation data for FLI, TL, and WIK.  The SNPfisher website includes the SNPfisher Variant Reporter tool, which provides the genomic position, alternate allele read frequency, strain specificity, restriction enzyme recognition site changes and flanking primers for all SNPs and Indels in a user-defined gene or region of the zebrafish genome. The SNPfisher site also contains links to display our SNP data in the UCSC genome browser.

  Butler MG, Iben JR, Marsden KC, Epstein JA, Granato M, Weinstein BM. 2015. SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. Development. 142: 1542-52.

  
  

• FishMap Zebrafish Genomics Knowledge base:

A community resource for Zebrafish Genomics.

Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S. FishMap Zv8 update--a genomic regulatory map of zebrafish. Zebrafish. 2010 Jun;7(2):179-80.

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• BLAST hits of Human Genes from Sanger sequence maintained by Zon lab:

  Each human gene annotated on the Santa Cruz site was compared by BLAST against the Sanger Institute zebrafish genome sequence. These data can be used to help identify zebrafish orthologues of human or Fugu genes.

• Zebrafish BLAST server at MGH:

  MGH site provides a BLAST search of a gene or marker of interest to the assembled sequence contigs of the zebrafish genomic shotgun sequence from the Sanger project.

• Tübingen Map of the Zebrafish Genome

• RH, meiotic and integrated maps of the genome:

  Centralized site for all meiotic and radiation hybrid maps of the zebrafish genome.

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• MGH Web-based Tool for Automating Primer Selection:

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•   Hopkins lab large insertional mutagenesis screen database : 

Detailed information on the mutants resulting from the large insertional mutagenesis screen described in Amsterdam, et al. (2004) Identification of 315 genes essential for early zebrafish development. Proceeding of the National Academy of Sciences 101: 12792-12797

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ZNP is a comprehensive resource for neurobehavioral and physiological data of adult zebrafish models. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models.

• Zebrafish Brain-Behavior Axis Database (ZBBAD)

  By gathering these literatures we tried to provide a package of neural studies on Zebrafish with behavioral outcomes and overseeing an intervention on the brain. The studies on zebrafish have different approaches, from neural disease and dysfunctionalities to the specific role of a neural factor. Near a half of the researchers used zebrafish to understand the brain functions, mechanisms, and their related gene expression patterns. However, some studies tried to improve imaging or other assessing tools. We included studies with any exposure, impacts the zebrafish's brain or behavior to gather all the recent methods and works in brain_behavior axes.

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