Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.
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DOI：
10.1093/molbev/msx148
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发表时间：
2017-08-01
影响因子：
10.7
通讯作者：
Bork P
中科院分区：
文献类型：
--
作者：
Huerta-Cepas J;Forslund K;Coelho LP;Szklarczyk D;Jensen LJ;von Mering C;Bork P
正交赋值非常适合于函数推理。然而，由于预测正交在大规模上是计算密集型的，并且大多数管线相对不可访问（例如，新的分配只能通过数据库更新获得），不太精确的基于同源性的功能转移仍然是（Meta）基因组注释的默认。因此，我们开发了eggNOG映射器，一个工具，用于功能注释的大集合的序列的基础上快速的正交分配使用预先计算的集群和eggNOG数据库的同源性。为了验证我们的方法，我们对两种广泛使用的基于同源性的方法：BLAST和InterProScan进行了基因本体论（GO）预测。应用于BLAST结果的正交滤波器将假阳性分配率降低了11%，并将实验验证的回收术语与每个蛋白质分配的所有术语的比率增加了15%。与InterProScan相比，eggNOG-mapper实现了相似的蛋白质组覆盖率和精确度，同时平均预测每个蛋白质多41个术语，并将每个蛋白质的总术语分配的实验验证术语回收率提高了35%。EggNOG-映射器预测得分在前5名的方法在三个GO类别使用CAFA 2 NK-部分基准。最后，我们评估了eggNOG映射器对宏基因组数据的功能注释，产生了比interProScan更好的性能。eggNOG-mapper的运行速度比BLAST快15倍，比InterProScan至少快2.5倍。该工具可以独立使用，也可以作为在线服务在http://eggnog-mapper.embl.de上使用。
Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g., new assignments only available through database updates), less precise homology-based functional transfer is still the default for (meta-)genome annotation. We, therefore, developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database. To validate our method, we benchmarked Gene Ontology (GO) predictions against two widely used homology-based approaches: BLAST and InterProScan. Orthology filters applied to BLAST results reduced the rate of false positive assignments by 11%, and increased the ratio of experimentally validated terms recovered over all terms assigned per protein by 15%. Compared with InterProScan, eggNOG-mapper achieved similar proteome coverage and precision while predicting, on average, 41 more terms per protein and increasing the rate of experimentally validated terms recovered over total term assignments per protein by 35%. EggNOG-mapper predictions scored within the top-5 methods in the three GO categories using the CAFA2 NK-partial benchmark. Finally, we evaluated eggNOG-mapper for functional annotation of metagenomics data, yielding better performance than interProScan. eggNOG-mapper runs ∼15× faster than BLAST and at least 2.5× faster than InterProScan. The tool is available standalone and as an online service at http://eggnog-mapper.embl.de.
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DOI：
10.1093/database/bar068
发表时间：
2012
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Burge S;Kelly E;Lonsdale D;Mutowo-Muellenet P;McAnulla C;Mitchell A;Sangrador-Vegas A;Yong SY;Mulder N;Hunter S
通讯作者：
Hunter S
影响因子：
3
作者：
Deegan (nee Clark), Jennifer I.;Dimmer, Emily C.;Mungall, Christopher J.
通讯作者：
Mungall, Christopher J.
影响因子：
12.3
作者：
Jiang Y;Oron TR;Clark WT;Bankapur AR;D'Andrea D;Lepore R;Funk CS;Kahanda I;Verspoor KM;Ben-Hur A;Koo da CE;Penfold-Brown D;Shasha D;Youngs N;Bonneau R;Lin A;Sahraeian SM;Martelli PL;Profiti G;Casadio R;Cao R;Zhong Z;Cheng J;Altenhoff A;Skunca N;Dessimoz C;Dogan T;Hakala K;Kaewphan S;Mehryary F;Salakoski T;Ginter F;Fang H;Smithers B;Oates M;Gough J;Törönen P;Koskinen P;Holm L;Chen CT;Hsu WL;Bryson K;Cozzetto D;Minneci F;Jones DT;Chapman S;Bkc D;Khan IK;Kihara D;Ofer D;Rappoport N;Stern A;Cibrian-Uhalte E;Denny P;Foulger RE;Hieta R;Legge D;Lovering RC;Magrane M;Melidoni AN;Mutowo-Meullenet P;Pichler K;Shypitsyna A;Li B;Zakeri P;ElShal S;Tranchevent LC;Das S;Dawson NL;Lee D;Lees JG;Sillitoe I;Bhat P;Nepusz T;Romero AE;Sasidharan R;Yang H;Paccanaro A;Gillis J;Sedeño-Cortés AE;Pavlidis P;Feng S;Cejuela JM;Goldberg T;Hamp T;Richter L;Salamov A;Gabaldon T;Marcet-Houben M;Supek F;Gong Q;Ning W;Zhou Y;Tian W;Falda M;Fontana P;Lavezzo E;Toppo S;Ferrari C;Giollo M;Piovesan D;Tosatto SC;Del Pozo A;Fernández JM;Maietta P;Valencia A;Tress ML;Benso A;Di Carlo S;Politano G;Savino A;Rehman HU;Re M;Mesiti M;Valentini G;Bargsten JW;van Dijk AD;Gemovic B;Glisic S;Perovic V;Veljkovic V;Veljkovic N;Almeida-E-Silva DC;Vencio RZ;Sharan M;Vogel J;Kansakar L;Zhang S;Vucetic S;Wang Z;Sternberg MJ;Wass MN;Huntley RP;Martin MJ;O'Donovan C;Robinson PN;Moreau Y;Tramontano A;Babbitt PC;Brenner SE;Linial M;Orengo CA;Rost B;Greene CS;Mooney SD;Friedberg I;Radivojac P
通讯作者：
Radivojac P
DOI：
10.1093/bioinformatics/btw183
发表时间：
2016-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Kultima JR;Coelho LP;Forslund K;Huerta-Cepas J;Li SS;Driessen M;Voigt AY;Zeller G;Sunagawa S;Bork P
通讯作者：
Bork P
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM