UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
复制标题
DOI：
10.1093/bioinformatics/btu739
复制
发表时间：
2015-03-15
期刊：
影响因子：
--
通讯作者：
UniProt Consortium
中科院分区：
文献类型：
--
作者：
Suzek BE;Wang Y;Huang H;McGarvey PB;Wu CH;UniProt Consortium
Motivation: UniRef databases provide full-scale clustering of UniProtKB sequences and are utilized for a broad range of applications, particularly similarity-based functional annotation. Non-redundancy and intra-cluster homogeneity in UniRef were recently improved by adding a sequence length overlap threshold. Our hypothesis is that these improvements would enhance the speed and sensitivity of similarity searches and improve the consistency of annotation within clusters. Results: Intra-cluster molecular function consistency was examined by analysis of Gene Ontology terms. Results show that UniRef clusters bring together proteins of identical molecular function in more than 97% of the clusters, implying that clusters are useful for annotation and can also be used to detect annotation inconsistencies. To examine coverage in similarity results, BLASTP searches against UniRef50 followed by expansion of the hit lists with cluster members demonstrated advantages compared with searches against UniProtKB sequences; the searches are concise (∼7 times shorter hit list before expansion), faster (∼6 times) and more sensitive in detection of remote similarities (>96% recall at e-value <0.0001). Our results support the use of UniRef clusters as a comprehensive and scalable alternative to native sequence databases for similarity searches and reinforces its reliability for use in functional annotation. Availability and implementation: Web access and file download from UniProt website at http://www.uniprot.org/uniref and ftp://ftp.uniprot.org/pub/databases/uniprot/uniref. BLAST searches against UniRef are available at http://www.uniprot.org/blast/ Contact: huang@dbi.udel.edu
登录
查看更多内容
DOI：
10.1016/s0097-8485(96)80004-0
发表时间：
1996-03-01
期刊：
COMPUTERS & CHEMISTRY
影响因子：
--
作者：
Gribskov, M;Robinson, NL
通讯作者：
Robinson, NL
影响因子：
3.4
作者：
Rivera AS;Pankey MS;Plachetzki DC;Villacorta C;Syme AE;Serb JM;Omilian AR;Oakley TH
通讯作者：
Oakley TH
影响因子：
14.9
作者：
Hunter S;Jones P;Mitchell A;Apweiler R;Attwood TK;Bateman A;Bernard T;Binns D;Bork P;Burge S;de Castro E;Coggill P;Corbett M;Das U;Daugherty L;Duquenne L;Finn RD;Fraser M;Gough J;Haft D;Hulo N;Kahn D;Kelly E;Letunic I;Lonsdale D;Lopez R;Madera M;Maslen J;McAnulla C;McDowall J;McMenamin C;Mi H;Mutowo-Muellenet P;Mulder N;Natale D;Orengo C;Pesseat S;Punta M;Quinn AF;Rivoire C;Sangrador-Vegas A;Selengut JD;Sigrist CJ;Scheremetjew M;Tate J;Thimmajanarthanan M;Thomas PD;Wu CH;Yeats C;Yong SY
通讯作者：
Yong SY
影响因子：
3
作者：
Capone G;Novello G;Fasano C;Trost B;Bickis M;Kusalik A;Kanduc D
通讯作者：
Kanduc D
影响因子：
3
作者：
Chang JM;Di Tommaso P;Taly JF;Notredame C
通讯作者：
Notredame C