SMART 7: recent updates to the protein domain annotation resource

被引：456

作者：

Letunic, Ivica ^{[1
]}

Doerks, Tobias ^{[1
]}

Bork, Peer ^{[1
]}

机构：

[1] European Mol Biol Lab, D-69012 Heidelberg, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

关键词：

INTERACTIVE TREE; DISPLAY; GENOMES; TOOL;

D O I：

10.1093/nar/gkr931

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

SMART (Simple Modular Architecture Research Tool) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 7 contains manually curated models for 1009 protein domains, 200 more than in the previous version. The current release introduces several novel features and a streamlined user interface resulting in a faster and more comfortable workflow. The underlying protein databases were greatly expanded, resulting in a 2-fold increase in number of annotated domains and features. The database of completely sequenced genomes now includes 1133 species, compared to 630 in the previous release. Domain architecture analysis results can now be exported and visualized through the iTOL phylogenetic tree viewer. 'metaSMART' was introduced as a novel subresource dedicated to the exploration and analysis of domain architectures in various metagenomics data sets. An advanced full text search engine was implemented, covering the complete annotations for SMART and Pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information.

引用

页码：D302 / D305

页数：4

共 19 条

[11] SMART 5: domains in the context of genomes and networks [J].

Letunic, Ivica ;

Copley, Richard R. ;

Pils, Birgit ;

Pinkert, Stefan ;

Schultz, Joerg ;

Bork, Peer .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D257-D260

[12]

Letunic I, 2011, NUCLEIC ACIDS RES, V39, pW475, DOI [10.1093/nar/gkr201, 10.1093/nar/gkr931]

[13] SMART 6: recent updates and new developments [J].

Letunic, Ivica ;

Doerks, Tobias ;

Bork, Peer .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D229-D232

[14] Database resources of the National Center for Biotechnology Information [J].

Sayers, Eric W. ;

Barrett, Tanya ;

Benson, Dennis A. ;

Bolton, Evan ;

Bryant, Stephen H. ;

Canese, Kathi ;

Chetvernin, Vyacheslav ;

Church, Deanna M. ;

DiCuccio, Michael ;

Federhen, Scott ;

Feolo, Michael ;

Fingerman, Ian M. ;

Geer, Lewis Y. ;

Helmberg, Wolfgang ;

Kapustin, Yuri ;

Landsman, David ;

Lipman, David J. ;

Lu, Zhiyong ;

Madden, Thomas L. ;

Madej, Tom ;

Maglott, Donna R. ;

Marchler-Bauer, Aron ;

Miller, Vadim ;

Mizrachi, Ilene ;

Ostell, James ;

Panchenko, Anna ;

Phan, Lon ;

Pruitt, Kim D. ;

Schuler, Gregory D. ;

Sequeira, Edwin ;

Sherry, Stephen T. ;

Shumway, Martin ;

Sirotkin, Karl ;

Slotta, Douglas ;

Souvorov, Alexandre ;

Starchenko, Grigory ;

Tatusova, Tatiana A. ;

Wagner, Lukas ;

Wang, Yanli ;

Wilbur, W. John ;

Yaschenko, Eugene ;

Ye, Jian .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D38-D51

[15] SMART, a simple modular architecture research tool: Identification of signaling domains [J].

Schultz, J ;

Milpetz, F ;

Bork, P ;

Ponting, CP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (11) :5857-5864

[16] The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored [J].

Szklarczyk, Damian ;

Franceschini, Andrea ;

Kuhn, Michael ;

Simonovic, Milan ;

Roth, Alexander ;

Minguez, Pablo ;

Doerks, Tobias ;

Stark, Manuel ;

Muller, Jean ;

Bork, Peer ;

Jensen, Lars J. ;

von Mering, Christian .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D561-D568

[17] Comparative metagenomics of microbial communities [J].

Tringe, SG ;

von Mering, C ;

Kobayashi, A ;

Salamov, AA ;

Chen, K ;

Chang, HW ;

Podar, M ;

Short, JM ;

Mathur, EJ ;

Detter, JC ;

Bork, P ;

Hugenholtz, P ;

Rubin, EM .

SCIENCE, 2005, 308 (5721) :554-557

[18] Community structure and metabolism through reconstruction of microbial genomes from the environment [J].

Tyson, GW ;

Chapman, J ;

Hugenholtz, P ;

Allen, EE ;

Ram, RJ ;

Richardson, PM ;

Solovyev, VV ;

Rubin, EM ;

Rokhsar, DS ;

Banfield, JF .

NATURE, 2004, 428 (6978) :37-43

[19] Environmental genome shotgun sequencing of the Sargasso Sea [J].

Venter, JC ;

Remington, K ;

Heidelberg, JF ;

Halpern, AL ;

Rusch, D ;

Eisen, JA ;

Wu, DY ;

Paulsen, I ;

Nelson, KE ;

Nelson, W ;

Fouts, DE ;

Levy, S ;

Knap, AH ;

Lomas, MW ;

Nealson, K ;

White, O ;

Peterson, J ;

Hoffman, J ;

Parsons, R ;

Baden-Tillson, H ;

Pfannkoch, C ;

Rogers, YH ;

Smith, HO .

SCIENCE, 2004, 304 (5667) :66-74

← 1 2 →