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

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/.

Figure 1.

Example tRNAscan-SE Search and Contextual Analysis. The Saccharomyces cerevisiae tRNA-Ser^CGA is analyzed using the tRNAscan-SE web server in default eukaryotic search mode. The red arrows show the analysis path from viewing the predicted tRNA results to finding the matching tRNA gene in GtRNAdb (3), to exploring the tRNA gene in context with tRNA modifications and gene expression data in the UCSC Genome Browser (10).