tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

Nucleic Acids Res. 2016 Jul 8;44(W1):W54-7. doi: 10.1093/nar/gkw413. Epub 2016 May 12.

Abstract

High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database. Previously, web-server tRNA detection was isolated from knowledge of existing tRNAs and their annotation. In this update of the tRNAscan-SE On-line resource, we tie together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers. The tRNAscan-SE On-line web server can be accessed at http://trna.ucsc.edu/tRNAscan-SE/.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Databases, Genetic
  • Genes, Fungal*
  • Humans
  • Internet
  • Nucleic Acid Conformation
  • RNA, Transfer / genetics*
  • Saccharomyces cerevisiae / genetics*
  • User-Computer Interface*

Substances

  • RNA, Transfer