The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

By P. Schattner, Angela N. Brooks, Todd M. Lowe. Nucleic Acids Res., 2005

2,175 citations recorded by the source corpus.

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 , and , respectively.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c23e93c75980c561bd74aa51640c96e134c6ab35

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Citations in the corpus

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “To increase the ease of use for scientists who cannot install and utilize UNIXbased software, the tRNAscan-SE On-line website (2,3) provides quick, in-depth tRNA analysis.”
MycoCosm portal: gearing up for 1000 fungal genomes (2013, background): “In addition to protein-coding genes, tRNAs are predicted using tRNAscan-SE (13).”
Tissue-Specific Differences in Human Transfer RNA Expression (2006, background): “Based on sequence conservation, most of the 42 probes for human nuclear encoded tRNAs should hybridize to mouse tRNAs as well as to some Drosophila and Caenorhabditis elegans tRNAs [4,5].”
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) (2013, methodology): “(3) Identify the tRNA and rRNA genes using ‘search_for_rnas’ (Niels Larsen, unpublished, available from the author on request), which uses tRNAscan-SE to find tRNAs (27) and BLASTN (19) against a set of RNA databases followed by endpoint adjustment to find rRNAs.”
The UCSC Genome Browser database: 2015 update (2014, background): “The UCSC Genes set includes both protein-coding and non-coding RNA genes from RefSeq, GenBank, the tRNA Genes track (31) and RFAM (32).”
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes (2016, methodology): “Similar to the original version of the tRNAscan-SE search server (4), users may select among multiple types of tRNAs (mixed/general, eukaryotic, bacterial, archaeal or mitochondrial) as well as different search modes to identify tRNA genes in their provided sequences.”
Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids (2015, methodology): “com/) using the plastid gene database described above and tRNAs were verified using tRNAscan (Schattner et al., 2005).”