The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

被引：250

作者：

Wilke, Andreas ^{[1
,2
]}

Harrison, Travis ^{[1
,2
]}

Wilkening, Jared ^{[1
,5
]}

Field, Dawn ^{[3
]}

Glass, Elizabeth M. ^{[1
,2
]}

Kyrpides, Nikos ^{[4
]}

Mavrommatis, Konstantinos ^{[4
]}

Meyer, Folker ^{[1
,2
,5
]}

机构：

[1] Argonne Natl Lab, Div Math & Comp Sci, Argonne, IL 60439 USA

[2] Univ Chicago, Computat Inst, Chicago, IL 60637 USA

[3] Ctr Ecol & Hydrol, Wallingford, Oxon, England

[4] Dept Energy Joint Genome Inst, Walnut Creek, CA USA

[5] Inst Genom & Syst Biol, Chicago, IL 60637 USA

来源：

BMC BIOINFORMATICS | 2012年 / 13卷

关键词：

IDENTIFIERS; GENOMES; BLAST; KEGG;

D O I：

10.1186/1471-2105-13-141

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Computing of sequence similarity results is becoming a limiting factor in metagenome analysis. Sequence similarity search results encoded in an open, exchangeable format have the potential to limit the needs for computational reanalysis of these data sets. A prerequisite for sharing of similarity results is a common reference. Description: We introduce a mechanism for automatically maintaining a comprehensive, non-redundant protein database and for creating a quarterly release of this resource. In addition, we present tools for translating similarity searches into many annotation namespaces, e.g. KEGG or NCBI's GenBank. Conclusions: The data and tools we present allow the creation of multiple result sets using a single computation, permitting computational results to be shared between groups for large sequence data sets.

引用

页数：5

共 20 条

[11] BioThesaurus: a web-based thesaurus of protein and gene names [J].

Liu, HF ;

Hu, ZZ ;

Zhang, J ;

Wu, C .

BIOINFORMATICS, 2006, 22 (01) :103-105

[12] The integrated microbial genomes (IMG) system [J].

Markowitz, Victor M. ;

Korzeniewski, Frank ;

Palaniappan, Krishna ;

Szeto, Ernest ;

Werner, Greg ;

Padki, Anu ;

Zhao, Xueling ;

Dubchak, Inna ;

Hugenholtz, Philip ;

Anderson, Iain ;

Lykidis, Athanasios ;

Mavromatis, Konstantinos ;

Ivanova, Natalia ;

Kyrpides, Nikos C. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D344-D348

[13] The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes [J].

Meyer, F. ;

Paarmann, D. ;

D'Souza, M. ;

Olson, R. ;

Glass, E. M. ;

Kubal, M. ;

Paczian, T. ;

Rodriguez, A. ;

Stevens, R. ;

Wilke, A. ;

Wilkening, J. ;

Edwards, R. A. .

BMC BIOINFORMATICS, 2008, 9 (1)

[14] FIGfams: yet another set of protein families [J].

Meyer, Folker ;

Overbeek, Ross ;

Rodriguez, Alex .

NUCLEIC ACIDS RESEARCH, 2009, 37 (20) :6643-6654

[15] eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations [J].

Muller, J. ;

Szklarczyk, D. ;

Julien, P. ;

Letunic, I. ;

Roth, A. ;

Kuhn, M. ;

Powell, S. ;

von Mering, C. ;

Doerks, T. ;

Jensen, L. J. ;

Bork, P. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D190-D195

[16] The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes [J].

Overbeek, R ;

Begley, T ;

Butler, RM ;

Choudhuri, JV ;

Chuang, HY ;

Cohoon, M ;

de Crécy-Lagard, V ;

Diaz, N ;

Disz, T ;

Edwards, R ;

Fonstein, M ;

Frank, ED ;

Gerdes, S ;

Glass, EM ;

Goesmann, A ;

Hanson, A ;

Iwata-Reuyl, D ;

Jensen, R ;

Jamshidi, N ;

Krause, L ;

Kubal, M ;

Larsen, N ;

Linke, B ;

McHardy, AC ;

Meyer, F ;

Neuweger, H ;

Olsen, G ;

Olson, R ;

Osterman, A ;

Portnoy, V ;

Pusch, GD ;

Rodionov, DA ;

Rückert, C ;

Steiner, J ;

Stevens, R ;

Thiele, I ;

Vassieva, O ;

Ye, Y ;

Zagnitko, O ;

Vonstein, V .

NUCLEIC ACIDS RESEARCH, 2005, 33 (17) :5691-5702

[17] Single-molecule sequencing of an individual human genome [J].

Pushkarev, Dmitry ;

Neff, Norma F. ;

Quake, Stephen R. .

NATURE BIOTECHNOLOGY, 2009, 27 (09) :847-U101

[18]

Rivest R, 1992, The MD5 message-digest algorithm, DOI DOI 10.17487/RFC1321

[19] MagicMatch - cross-referencing sequence identifiers across databases [J].

Smith, M ;

Kunin, V ;

Goldovsky, L ;

Enright, AJ ;

Ouzounis, CA .

BIOINFORMATICS, 2005, 21 (16) :3429-3430

[20] The COG database: an updated version includes eukaryotes [J].

Tatusov, RL ;

Fedorova, ND ;

Jackson, JD ;

Jacobs, AR ;

Kiryutin, B ;

Koonin, EV ;

Krylov, DM ;

Mazumder, R ;

Mekhedov, SL ;

Nikolskaya, AN ;

Rao, BS ;

Smirnov, S ;

Sverdlov, AV ;

Vasudevan, S ;

Wolf, YI ;

Yin, JJ ;

Natale, DA .

BMC BIOINFORMATICS, 2003, 4 (1)

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