Genomic Resources for Zebrafish

Genome and Map Resources Additional DAS tracks with SNP and indel analysis derived from the comparison of the whole genome shotgun reads are available. Ensembl also offers completely customizable downloads with EnsMart
You can search Ensembl with either Blast or SSAHA.
  • Additional services available at the Sanger Institute
  • 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:
    Custom annotation tracks for the zebrafish research community include:
  • Zebrafish Genome Resources at NCBI
  • 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.

  • Zebrafish Mutant Mapping Facility: This facility provides mutant mapping services to the zebrafish community.

    Primers

  • Automatic zebrafish-specific PCR primer design service:
    This service provides "one stop shopping" for picking primers, BLAST of primer sequences for specificity against the latest zebrafish genome sequence, and graphical views of the locations of primers with different confidence levels. All you need is a few clicks. No more cutting and pasting from one website to another. The program flows automatically. Detailed information for use of this program can be found in the "general info" and "help file".
  • MGH web-based tool for automating primer selection:
    MGH site offers this tool which searches for a supercontig, scaffold, or finished BAC clone by name or accession number, derives all di- and tri- nucleotide repeat sequences in the supercontig, masks the sequence around the repeats for larger zebrafish repetitive sequences and then designs unique sequence primer pairs to amplify the simple sequence repeats. These are potentially polymorphic simple sequence repeats (SSRs) that can be used in genetic mapping/positional cloning projects. The site also offers a tool to process your sequence for simple repeats/primer generation

    • Microarrays

  • Zebrafish Affy Chip Annotation Project:
    The Trans-NIH Zebrafish Genome Initiative at Children's Hospital Boston aims to annotate zebrafish genes with human known genes for functional and comparative studies. This website provides a new web service for retrieving hand-annotated zebrafish genes represented on the Affymetrix Zebrafish Genome Array to the research community. A total of 11074 probesets from the complete set of 15617 (115 of which are controls) have been manually annotated with human known genes (UCSC HG16). We are currently manually annotating the remaining probesets which have putative Zv6 Genscan human-zebrafish orthologs. We will continue annotating as new sequence data become available and by comparative genomics approaches. Researchers can choose to download the entire annotation as a text file, or retrieve their specific gene probes of interest by submitting a list of Affymetrix probeset IDs of interest.

    The latest release is now available at http://134.174.23.160/zfACA/hash/cumulative_expanded.aspx.

  • University of Massachusetts Medical School Zebrafish Microarray Database:
    To access microarray data type username: "guest", password: "password"; once you have logged on, click on "Analysis" in the upper right hand corner. Covassin, L., Amigo, J.D., Suzuki, K., Teplyuk, V., Straubhaar, J., and Lawson, N.D. (2006) Global analysis of hematopoietic and vascular endothelial gene expression by tissue specific microarray profiling in zebrafish. Dev. Biol. 299(2): 551-562
  • DNA Microarray Data from Amacher, Farber and Ho labs
  • Microarray expression at ZF-Espresso
  • Zebrafish Oligonucleotide Arrays:
    The Norwegian Microarray Consortium offers their array products for academic use to customers world wide. One limitation is oligonucleotide arrays, which cannot provided to users in the US and Japan, due to licensing conditions. A moderate license fee will be added to the base price for oligonucleotide arrays sold to users in the UK, France, Germany, Italy, Austria, Belgium, Sweden, Switzerland, Luxembourg, and The Netherlands.
  • Zebrafish Compugen microarray annotation database:
    Compugen array clones are annotated at this site. The GenBank id of genes in the Compugen oligo list can be used to access information from Unigene, Entrez Gene, Gene Ontology, human and mouse HomoloGene, Unigene protein similarities of mouse and human, ZGI index. The gene chromosomal location is also available. The details of the microarray annotation database are published in PLoS Genetics (2005).
    • cDNA and EST Resources

    Stock Centers

    Mutagenesis Projects

    Gene and Enhancer Traps

    Morpholinos

    Pathways

    White Papers