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Zebra Finch Genome & Analysis Tools


Zebra finch genome (Ensembl).  Ensembl provides the "official" annotation of genes, RNAs and proteins, and has a number of tools for comparative analyses across species.  Details of Ensembl annotations may change over time, as Ensembl periodically issues new updated "builds" for the entire database (of all species). Annotations and other data can be easily downloaded in bulk using Biomart.


Zebra finch genome browser (UCSC).  This takes you to the UCSC genome browser for the zebra finch. The core sequence information and annotations are basically the same as in the Ensembl site above, but some people find the USCS browser more "user friendly." Additionally, the UCSC browser allows one to upload and store data in the form of customized  "tracks" that display alongside the standard tracks visible to everyone.


Songbirdtranscriptome and ESTIMA databases.  These two databases of zebra finch brain cDNAs predated the genome annotation and may still be useful, although much of this information (and more) has been incorporated into the annotations available on the Ensembl and UCSC genome browsers above. 


Zebra finch GO analysis tool: Here you can test for statistical enrichment or impoverishment of Gene Ontology (GO) annotation terms in a list of genes of interest. You paste in a list of Ensembl gene Identifiers, and a reference set of gene identifiers (default is the entire genome), and you quickly get back a list of all the GO terms associated with the genes in your list, their frequencies in your list and in the reference set, and the results of statistical tests for the significance of the differences in these frequencies. This site is maintained by Mick Watson at ARK/Roslin, specifically for the zebra finch community.


Zebra finch transcription factor binding site enrichment tool  This tool tests for statistical enrichment or impoverishment of predicted transcription factor binding sites, associated with a list of genes. The methods for this are described in the Supplementary material for the zebra finch genome paper (Warren et al., 2010), and were developed by Saurabh Sinha (U. of Illinois).


Zebra Finch Genome Resources: Information on zebra finch and avian-related resources from NCBI and the zebra finch research community. Resources include Blasting against zebra finch genome and trace archives, as well as links to other avian sequence resources and white papers. 




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