Journal article

KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome

Walter C Dunlap, Antonio Starcevic, Damir Baranasic, Janko Diminic, Jurica Zucko, Ranko Gacesa, Madeleine JH van Oppen, Daslav Hranueli, John Cullum, Paul F Long

BMC GENOMICS | BMC | Published : 2013

Abstract

BACKGROUND: Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION: Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic a..

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University of Melbourne Researchers

Grants

Awarded by Biotechnology and Biological Sciences Research Council of the United Kingdom (BBSRC)


Awarded by Croatian Science Foundation


Awarded by Biotechnology and Biological Sciences Research Council


Awarded by Medical Research Council


Funding Acknowledgements

The authors are indebted to Professor Noriyuki Satoh and his research team at the Marine Genomics Unit, Okinawa Institute of Science and Technology, Japan for making the protein sequence of A. digitifera publically available without restriction of use. We thank the following scientists from the Australian Institute of Marine Science for helpful discussions, Dr David Bourne, Dr Andrew Negri, Dr Elisha Wood-Charlson and Dr Karen Weynberg. We are also grateful to Dr Bill Leggat of the ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Australia for critically reviewing this manuscript. Financial support for this work has come from the Biotechnology and Biological Sciences Research Council of the United Kingdom (BBSRC grant BB/H010009/2 to WCD and PFL); from the Australian Institute of Marine Science (WCD and MvO); from a cooperation grant of the German Academic Exchange Service (DAAD) and Ministry of Science, Education and Sports, Republic of Croatia (to JC and DH) and from the Croatian Science Foundation (grant 09/5 to DH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.