The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
Open accessAbstract
Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at http://lowelab.ucsc.edu/tRNAscan-SE/, http://lowelab.ucsc.edu/snoscan/ and http://lowelab.ucsc.edu/snoGPS/, respectively.
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International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Self-citationtRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 10,905
Self-citationRNA sequence analysis using covariance models
Eddy, S. R., & Durbin, R. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.11.2079 · Cited by 793
A Computational Screen for Methylation Guide snoRNAs in Yeast
Lowe, T. M., & Eddy, S. R. (1999) · Science · doi:10.1126/science.283.5405.1168 · Cited by 465
Self-citationHomologs of Small Nucleolar RNAs in Archaea
Omer, A. D., Lowe, T. M., Russell, A. G., Ebhardt, H., Eddy, S. R., & Dennis, P. P. (2000) · Science · doi:10.1126/science.288.5465.517 · Cited by 349
Self-citationHuttenhofer, A. (2001) · The EMBO Journal · doi:10.1093/emboj/20.11.2943 · Cited by 326
RNA-guided Nucleotide Modification of Ribosomal and Other RNAs
Decatur, W. A., & Fournier, M. J. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.r200023200 · Cited by 214
Clouet-d’Orval, B. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.22.4518 · Cited by 158
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Self-citationA guided tour: small RNA function in Archaea
Dennis, P. P., Omer, A. D., & Lowe, T. M. (2001) · Molecular Microbiology · doi:10.1046/j.1365-2958.2001.02381.x · Cited by 138
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Self-citationtRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab688 · Cited by 1,925
Self-citationMycoCosm portal: gearing up for 1000 fungal genomes
Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1183 · Cited by 1,498
The UCSC Genome Browser database: 2015 update
Rosenbloom, K. R., Armstrong, J., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1177 · Cited by 874
Metadata
- Authors
- Schattner, P., Brooks, A. N., & Lowe, T. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-07-01
- Volume
- 33
- Issue
- Web Server
- Pages
- W686-W689
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2033713984
- Cited by
- 2,295
- References
- 15
- FWCI
- 3.23
- Type
- journal article
- Language
- en
- Open access
- gold
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