The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
Open accessAbstract
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.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
KEGG for linking genomes to life and the environment
Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm882 · Cited by 6,782
The Gene Ontology (GO) database and informatics resource
Gene Ontology Consortium (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh036 · Cited by 4,579
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,430
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
Self-citationThe MD5 Message-Digest Algorithm
Rivest (1992) · Medical Entomology and Zoology · Cited by 2,853
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki866 · Cited by 2,012
Kanehisa, M. (2002) · Novartis Foundation Symposia · doi:10.1002/0470857897.ch8 · Cited by 1,383
WormBase: a multi-species resource for nematode biology and genomics
Harris, T. W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh066 · Cited by 715
Cited by
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Stewart, R. D., Auffret, M. D., Warr, A., Wiser, A. H., Press, M. O., Langford, K. W., Liachko, I., Snelling, T. J., Dewhurst, R. J., Walker, A. W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03317-6 · Cited by 559
MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function
Keegan, K. P., Glass, E. M., & Meyer, F. (2016) · Methods in Molecular Biology · doi:10.1007/978-1-4939-3369-3_13 · Cited by 477
Self-citationTu, Q., Lin, L., Cheng, L., Deng, Y., & He, Z. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty741 · Cited by 470
An evaluation of the accuracy and speed of metagenome analysis tools
Lindgreen, S., Adair, K. L., & Gardner, P. P. (2016) · Scientific Reports · doi:10.1038/srep19233 · Cited by 331
Metadata
- Authors
- Wilke, A., Harrison, T., Wilkening, J., Field, D., Glass, E. M., Kyrpides, N., Mavrommatis, K., & Meyer, F.
- Venue
- BMC Bioinformatics
- Published
- 2012-06-21
- Volume
- 13
- Issue
- 1
- Pages
- 141-141
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2041117131
- Cited by
- 314
- References
- 19
- FWCI
- 5.34
- Type
- journal article
- Language
- en
- Open access
- gold
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- Wilke, A., Harrison, T., Wilkening, J., Field, D., Glass, E. M., Kyrpides, N., Mavrommatis, K., & Meyer, F. (2012). The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-13-141
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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