追求同源物的社区标准。
Toward community standards in the quest for orthologs.
出版信息
Bioinformatics. 2012 Mar 15;28(6):900-4. doi: 10.1093/bioinformatics/bts050. Epub 2012 Feb 12.
Abstract
The identification of orthologs-genes pairs descended from a common ancestor through speciation, rather than duplication-has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second 'Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications.
摘要
通过物种形成，从共同祖先传承下来的直系同源基因对的鉴定，而不是通过复制，已经成为许多生物信息学应用的重要组成部分，从新基因组的注释到实验目标的优先级排序。然而，直系同源推断方法的开发和应用受到缺乏共识的源蛋白质组、文件格式和基准的阻碍。第二次“寻找直系同源物”会议汇集了来自不同领域的利益相关者，以解决这些挑战。我们报告了这次会议的成果和结果，重点关注对广大研究界特别相关的主题。寻找直系同源物联盟是一个开放的社区，欢迎所有对直系同源研究和应用感兴趣的研究人员做出贡献。
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本文引用的文献
1
Overview and comparison of ortholog databases.
Drug Discov Today Technol. 2006 Summer;3(2):137-43. doi: 10.1016/j.ddtec.2006.06.002.
2
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase.
Genome Biol. 2012 Feb 22;13(2):R12. doi: 10.1186/gb-2012-13-2-r12.
3
Editorial: Orthology and applications.
Brief Bioinform. 2011 Sep;12(5):375-6. doi: 10.1093/bib/bbr057.
4
RNAcentral: A vision for an international database of RNA sequences.
RNA. 2011 Nov;17(11):1941-6. doi: 10.1261/rna.2750811. Epub 2011 Sep 22.
5
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6
Orthology prediction methods: a quality assessment using curated protein families.
Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011 Aug 19.
7
Domain architecture conservation in orthologs.
BMC Bioinformatics. 2011 Aug 5;12:326. doi: 10.1186/1471-2105-12-326.
8
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.
Brief Bioinform. 2011 Sep;12(5):423-35. doi: 10.1093/bib/bbr034. Epub 2011 Jul 7.
9
Testing the ortholog conjecture with comparative functional genomic data from mammals.
PLoS Comput Biol. 2011 Jun;7(6):e1002073. doi: 10.1371/journal.pcbi.1002073. Epub 2011 Jun 9.
10
Computational methods for Gene Orthology inference.
Brief Bioinform. 2011 Sep;12(5):379-91. doi: 10.1093/bib/bbr030. Epub 2011 Jun 19.
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