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Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB)

Rebecca E. Foulger¹ and UniProt Consortium²

Correspondence: (Login to view email address)

1. European Bioinformatics Institute (EMBL-EBI)
2. European Bioinformatics Institute (EMBL-EBI), Swiss Institute of Bioinformatics (SIB), Protein Information Resource (PIR)

PPT (2.7 MB) PDF (889.5 KB)

Document Type:

Poster

Date:

Received 23 April 2009 10:30 UTC; Posted 23 April 2009

Subjects:

Genetics & Genomics, Bioinformatics

Tags:

• Xenopus
• zebrafish
• curation
• biocuration
• protein
• database
• uniprot
• UniProtKB
• Swiss-Prot
• ZFIN

Abstract:

The African clawed frog Xenopus laevis and the zebrafish Danio rerio have both proved to be good model organisms for studying early vertebrate cellular and developmental biology. More recently, the related western clawed frog Xenopus tropicalis has become a popular choice in the laboratory, since its shorter life style and diploid genome make it more amenable to genetic analysis. Ongoing sequencing of the X. tropicalis and D. rerio genomes, together with the growing number of EST/cDNA projects, is generating large amounts of sequence data and revealing many human developmental and disease genes that have counterparts in fish and frog.

UniProtKB/Swiss-Prot curates Xenopus and zebrafish proteins with functional and sequence annotation from the literature and sequence analysis tools, using both controlled vocabularies (including GO terms) and free text. The tetraploid nature of the X. laevis and D. rerio genomes complicates annotation since the protein copies need to be identified and curated as separate UniProtKB/Swiss-Prot entries. The recent addition of Xenbase cross-references in Xenopus UniProtKB entries has been the result of cross-talk with Xenbase, and we continue to collaborate with ZFIN to ensure consistency between databases.

UniProt is mainly supported by the NIH, European Commission FELICS, Swiss Federal Government, PATRIC BRC and NSF grants.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Foulger, Rebecca and Consortium, UniProt. Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB). Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3153.1> (2009)

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