Genomics Resources

Title Description A website for investigating available avian genomes and transcriptome sequences for comparative genome analyses.
Ensembl: Zebra Finch First release of the high-coverage ~6X assembly of the Zebra finch (Taeniopygia guttata) genome (see also UCSC BLAT Browser).
UCSC ZF Blat Browser Browser for BLAT mapping sequences to the Jul. 2008 Taeniopygia guttata draft v3.2.4 genome assembly (and other species).

Transcriptomics Resources

Title Description
Brain Transcriptome Library Database of songbird cDNA clone information (Jarvis lab; Duke University). Clones are annotated with behavioral information, and are linked to information about homologous genes in other species.
Estima: Songbird Song Neurogenomics Consortion (SoNG) cDNA resource.
CUGI BAC/EST Resources Offers the development and distribution of high quality genomic and bioinformatic tools and services for the life science community.
NCBI ZF Nucleotide BLAST Zebra Finch Nucleotide BLAST search

Title Description
Avian Brain Nomenclature Provides background and information on the revised avian brain nomenclature (
The Zebra Finch Brain Atlas An online atlas of the zebra finch brain courtesy of Harvey Karten and colleagues (Nissl and Myelin stains; 3 planes).
MRI Atlas of the zebra finch brain MRI atlas of the zebra finch brain.

Title Description
Songbirdscience A shared resource for birdsong scientists to discuss and explore topics and resources in songbird biology.
NCBI: Zebra finch Homepage dedicated to providing information about zebra finch- and avian-related resources from NCBI and the zebra finch research community.
ZF KEGG Pathway Database Zebra finch specific KEGG Pathway maps assembled from RefSeqs information.
NCBI: Gene Information from a wide range of species. Records include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

Title Description
Ensembl: Chicken The 2.1 (May 2006) release of the chicken genome.
GEISHA Online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development

Title Description Digital atlas of gene expression patterns in the mouse.
The Allen Mouse Brain Atlas Genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain. is an interactive multiresolution next-generation brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet.
Mouse Connectome The Mouse Connectome Project (MCP) aims to create a three-dimensional digital connectome atlas of the C57Black/6J mouse brain.
Mouse Brain Architecture Project is a work in progress, an evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain’s organization, and what the evidence is for that knowledge.

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