联手寻找直系同源物。
Joining forces in the quest for orthologs.
出版信息
Genome Biol. 2009;10(9):403. doi: 10.1186/gb-2009-10-9-403. Epub 2009 Sep 29.
Abstract
Better orthology-prediction resources would be beneficial for the whole biological community. A recent meeting discussed how to coordinate and leverage current efforts.
摘要
更好的同源物预测资源将有益于整个生物界。最近的一次会议讨论了如何协调和利用当前的努力。
相似文献
1
Joining forces in the quest for orthologs.联手寻找直系同源物。
Genome Biol. 2009;10(9):403. doi: 10.1186/gb-2009-10-9-403. Epub 2009 Sep 29.
2
Standardized benchmarking in the quest for orthologs.寻找直系同源基因过程中的标准化基准测试。
Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.
3
Deep Omics.深度组学。
Proteomics. 2018 Jan;18(2). doi: 10.1002/pmic.201700319. Epub 2017 Dec 29.
4
Advances and Applications in the Quest for Orthologs.同源基因的探索、发展与应用。
Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150.
5
Function prediction and protein networks.功能预测与蛋白质网络
Curr Opin Cell Biol. 2003 Apr;15(2):191-8. doi: 10.1016/s0955-0674(03)00009-7.
6
Big data and other challenges in the quest for orthologs.大数据和其他挑战在寻找直系同源基因的过程中。
Bioinformatics. 2014 Nov 1;30(21):2993-8. doi: 10.1093/bioinformatics/btu492. Epub 2014 Jul 26.
7
Inferring Orthology and Paralogy.推断直系同源和旁系同源关系。
Methods Mol Biol. 2019;1910:149-175. doi: 10.1007/978-1-4939-9074-0_5.
8
Integrative database analysis in structural genomics.结构基因组学中的综合数据库分析
Nat Struct Biol. 2000 Nov;7 Suppl:960-3. doi: 10.1038/80739.
9
New metrics for comparative genomics.用于比较基因组学的新指标。
Curr Opin Biotechnol. 2006 Oct;17(5):440-7. doi: 10.1016/j.copbio.2006.08.007. Epub 2006 Sep 15.
10
Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.在直系同源基因簇（COGs）数据库中检测非直系同源关系，以及使用特定基因组最佳匹配来对直系同源基因进行分组的其他方法。
Nucleic Acids Res. 2006 Jul 11;34(11):3309-16. doi: 10.1093/nar/gkl433. Print 2006.
引用本文的文献
1
Synthetic lethality and the minimal genome size problem.合成致死性与最小基因组大小问题。
mSphere. 2024 Jul 30;9(7):e0013924. doi: 10.1128/msphere.00139-24. Epub 2024 Jun 21.
2
OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes.OrthoVenn3：一个用于跨基因组探索和可视化同源数据的集成平台。
Nucleic Acids Res. 2023 Jul 5;51(W1):W397-W403. doi: 10.1093/nar/gkad313.
3
HGD: an integrated homologous gene database across multiple species.HGD：一个跨物种的同源基因数据库。
Nucleic Acids Res. 2023 Jan 6;51(D1):D994-D1002. doi: 10.1093/nar/gkac970.
4
Ten Years of Collaborative Progress in the Quest for Orthologs.寻找同源基因的十年协同进展。
Mol Biol Evol. 2021 Jul 29;38(8):3033-3045. doi: 10.1093/molbev/msab098.
5
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench.基准测试 Orthogroup 推断准确性：重新审视 Orthobench。
Genome Biol Evol. 2020 Dec 6;12(12):2258-2266. doi: 10.1093/gbe/evaa211.
6
The Quest for Orthologs benchmark service and consensus calls in 2020.2020 年寻找直系同源物基准服务和共识调用。
Nucleic Acids Res. 2020 Jul 2;48(W1):W538-W545. doi: 10.1093/nar/gkaa308.
7
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.MetaPhOrs 2.0：基于系统发育的综合方法，推断生命之树上的直系同源和旁系同源。
Nucleic Acids Res. 2020 Jul 2;48(W1):W553-W557. doi: 10.1093/nar/gkaa282.
8
Genome-wide identification and characterization of the MADS-box gene family in .. 中MADS盒基因家族的全基因组鉴定与特征分析
PeerJ. 2019 Nov 7;7:e8019. doi: 10.7717/peerj.8019. eCollection 2019.
9
Advances and Applications in the Quest for Orthologs.同源基因的探索、发展与应用。
Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150.
10
SonicParanoid: fast, accurate and easy orthology inference.SonicParanoid：快速、准确、易用的直系同源推断。
Bioinformatics. 2019 Jan 1;35(1):149-151. doi: 10.1093/bioinformatics/bty631.
本文引用的文献
1
Overview and comparison of ortholog databases.直系同源数据库概述与比较
Drug Discov Today Technol. 2006 Summer;3(2):137-43. doi: 10.1016/j.ddtec.2006.06.002.
2
ProGMap: an integrated annotation resource for protein orthology.ProGMap：蛋白质直系同源性的综合注释资源。
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W428-34. doi: 10.1093/nar/gkp462. Epub 2009 Jun 3.
3
Berkeley PHOG: PhyloFacts orthology group prediction web server.伯克利PHOG：系统发育事实直系同源组预测网络服务器。
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W84-9. doi: 10.1093/nar/gkp373. Epub 2009 May 12.
4
Phylogenetic and functional assessment of orthologs inference projects and methods.直系同源物推断项目和方法的系统发育与功能评估。
PLoS Comput Biol. 2009 Jan;5(1):e1000262. doi: 10.1371/journal.pcbi.1000262. Epub 2009 Jan 16.
5
Algorithm of OMA for large-scale orthology inference.用于大规模直系同源推断的OMA算法。
BMC Bioinformatics. 2008 Dec 4;9:518. doi: 10.1186/1471-2105-9-518.
6
Large-scale assignment of orthology: back to phylogenetics?大规模同物异名分配：回归系统发育学？
Genome Biol. 2008 Oct 30;9(10):235. doi: 10.1186/gb-2008-9-10-235.
7
The quest for orthologs: finding the corresponding gene across genomes.寻找直系同源基因：在不同基因组中找到对应的基因。
Trends Genet. 2008 Nov;24(11):539-51. doi: 10.1016/j.tig.2008.08.009. Epub 2008 Sep 24.
8
The HGNC Database in 2008: a resource for the human genome.2008年的HGNC数据库：人类基因组资源
Nucleic Acids Res. 2008 Jan;36(Database issue):D445-8. doi: 10.1093/nar/gkm881. Epub 2007 Nov 4.
9
eggNOG: automated construction and annotation of orthologous groups of genes.蛋酒（EggNOG）：直系同源基因簇的自动构建与注释
Nucleic Acids Res. 2008 Jan;36(Database issue):D250-4. doi: 10.1093/nar/gkm796. Epub 2007 Oct 16.
10
Assessing performance of orthology detection strategies applied to eukaryotic genomes.评估应用于真核生物基因组的直系同源检测策略的性能。
PLoS One. 2007 Apr 18;2(4):e383. doi: 10.1371/journal.pone.0000383.
Zotero 插件