The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
SUPERFAMILY 1.75 including a domain-centric gene ontology method
Open accessAbstract
The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 metagenomes and other gene collections such as UniProt. All models and assignments are available to browse and download at http://supfam.org. A new hidden Markov model library based on SCOP 1.75 has been created and a previously ignored class of SCOP, coiled coils, is now included. Our scoring component now uses HMMER3, which is in orders of magnitude faster and produces superior results. A cloud-based pipeline was implemented and is publicly available at Amazon web services elastic computer cloud. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life. The most significant advance in SUPERFAMILY is that now it contains a domain-based gene ontology (GO) at the superfamily and family levels. A new methodology was developed to ensure a high quality GO annotation. The new methodology is general purpose and has been used to produce domain-based phenotypic ontologies in addition to GO.
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Cites
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
The Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694
Direct detection of DNA methylation during single-molecule, real-time sequencing
Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460
The human phenotype ontology: a tool for annotating and analyzing human hereditary disease
Robinson, P. N., Köhler, S., Bauer, S., Seelow, D., Horn, D., & Mundlos, S. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.09.017 · Cited by 1,034
Computational solutions to large‐scale data management and analysis
Schadt, E. E., Linderman, M. D., Sorenson, J., Lee, L., & Nolan, G. P. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2857 · Cited by 631
The mammalian phenotype ontology: enabling robust annotation and comparative analysis
Smith, C. L., & Eppig, J. T. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.44 · Cited by 353
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HMMER web server: interactive sequence similarity searching
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A large-scale evaluation of computational protein function prediction
Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2340 · Cited by 1,028
Self-citationD2P2: database of disordered protein predictions
Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., Dosztányi, Z., Uversky, V. N., Obradovic, Z., Kurgan, L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1226 · Cited by 705
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(2023) · doi:10.3390/ijms241311007 · Cited by 15
Metadata
- Authors
- de Lima Morais, D. A., Fang, H., Rackham, O. J. L., Wilson, D., Pethica, R., Chothia, C., & Gough, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-11-09
- Volume
- 39
- Issue
- Database
- Pages
- D427-D434
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2151946481
- Cited by
- 178
- References
- 6
- FWCI
- 5.91
- Type
- journal article
- Language
- en
- Open access
- gold
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- de Lima Morais, D. A., Fang, H., Rackham, O. J. L., Wilson, D., Pethica, R., Chothia, C., & Gough, J. (2011). SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Research. https://doi.org/10.1093/nar/gkq1130
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
