The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.
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博洛尼亚注释资源（BAR 3.0）：改善蛋白质功能注释。
DOI：
10.1093/nar/gkx330
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发表时间：
2017-07-03
影响因子：
14.9
通讯作者：
Casadio R
中科院分区：
文献类型：
--
作者：
Profiti G;Martelli PL;Casadio R
BAR 3.0 更新了我们的服务器 BAR（博洛尼亚注释资源），用于根据序列预测蛋白质结构和功能特征。我们增加数据量、查询能力以及向用户传达的信息。 BAR 3.0 的核心是 UniProtKB 序列的基于图的聚类程序，遵循严格的成对相似性标准（序列同一性≥40%，比对覆盖率≥90%）。每个集群包含从 UniProtKB、GO、PFAM 和 PDB 下载的可用注释。经过统计验证后，GO 术语和 PFAM 域是特定于簇的，并在满足相似性约束后注释进入簇的新序列。 BAR 3.0 包括 1 361 773 个簇中的 28 869 663 个序列，其中 22.2%（22 241 661 个序列）和 47.4%（24 555 055 个序列）分别具有至少一个经过验证的 GO 术语和一个 PFAM 结构域。 1.4% 的簇（所有序列的 36%）包含 PDB 结构，并且该簇与隐马尔可夫模型相关联，该模型允许构建适合结构建模的模板-目标比对。其他一些 3 399 026 个序列是单例。 BAR 3.0 提供了改进的搜索界面，允许通过 UniProtKB-accession、Fasta 序列、GO-term、PFAM-domain、有机体、PDB 和配体进行查询。在 CAFA2 目标上进行评估时，BAR 3.0 在很大程度上优于我们之前的版本，并且在最先进的方法中得分。 BAR 3.0 已公开发布，可通过 http://bar.biocomp.unibo.it/bar3 访问。
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3.
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影响因子：
14.9
作者：
Mitchell A;Chang HY;Daugherty L;Fraser M;Hunter S;Lopez R;McAnulla C;McMenamin C;Nuka G;Pesseat S;Sangrador-Vegas A;Scheremetjew M;Rato C;Yong SY;Bateman A;Punta M;Attwood TK;Sigrist CJ;Redaschi N;Rivoire C;Xenarios I;Kahn D;Guyot D;Bork P;Letunic I;Gough J;Oates M;Haft D;Huang H;Natale DA;Wu CH;Orengo C;Sillitoe I;Mi H;Thomas PD;Finn RD
通讯作者：
Finn RD
影响因子：
4.4
作者：
Bartoli, Lisa;Montanucci, Ludovica;Casadio, Rita
通讯作者：
Casadio, Rita
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
影响因子：
14.9
作者：
Orchard S;Ammari M;Aranda B;Breuza L;Briganti L;Broackes-Carter F;Campbell NH;Chavali G;Chen C;del-Toro N;Duesbury M;Dumousseau M;Galeota E;Hinz U;Iannuccelli M;Jagannathan S;Jimenez R;Khadake J;Lagreid A;Licata L;Lovering RC;Meldal B;Melidoni AN;Milagros M;Peluso D;Perfetto L;Porras P;Raghunath A;Ricard-Blum S;Roechert B;Stutz A;Tognolli M;van Roey K;Cesareni G;Hermjakob H
通讯作者：
Hermjakob H
影响因子：
3
作者：
Piovesan D;Profiti G;Martelli PL;Casadio R
通讯作者：
Casadio R