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

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 fu...

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Main Authors:	Lowe, Todd M., Chan, Patricia P.
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987944/

id	pubmed-4987944
recordtype	oai_dc
spelling	pubmed-49879442016-08-22 tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes Lowe, Todd M. Chan, Patricia P. Web Server issue 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/. Oxford University Press 2016-07-08 2016-05-12 /pmc/articles/PMC4987944/ /pubmed/27174935 http://dx.doi.org/10.1093/nar/gkw413 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Lowe, Todd M. Chan, Patricia P.
spellingShingle	Lowe, Todd M. Chan, Patricia P. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
author_facet	Lowe, Todd M. Chan, Patricia P.
author_sort	Lowe, Todd M.
title	tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
title_short	tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
title_full	tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
title_fullStr	tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
title_full_unstemmed	tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
title_sort	trnascan-se on-line: integrating search and context for analysis of transfer rna genes
description	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/.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987944/
_version_	1613628928920911872

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

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