Abstract
AbstractThe 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.
Highlights
Introduction toUniProt UniProt (Universal Protein Resource: http://www.uniprot.org) provides a central resource of protein sequences with functional annotation
The UniProt Consortium is a collaboration between the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR)
PubMed searches, requests from users, crossreference updates and sequence revisions are all used to identify which proteins are of priority to curate
Summary
UniProt (Universal Protein Resource: http://www.uniprot.org) provides a central resource of protein sequences with functional annotation. The UniProt Consortium is a collaboration between the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR). UniProt Knowledgebase (UniProtKB) contains the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section. For both Xenopus and zebrafish, protein and gene nomenclature is generally propagated from the human ortholog, with species-specific names added as synonyms. We use a protein-by-protein approach to curation. PubMed searches, requests from users, crossreference updates and sequence revisions are all used to identify which proteins are of priority to curate. Entries are curated using our flat-file editor, CRiSP
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
