publication . Other literature type . Article . 2016

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

Todd M Lowe; Patricia P Chan;
  • Published: 01 May 2016
  • Publisher: Oxford University Press (OUP)
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 lin...
Subjects
free text keywords: Genome, Molecular biology, Genetics, Biology, Genome project, Gene, RNA, Web server, computer.software_genre, computer, DNA sequencing, Transfer RNA, Annotation, Web Server issue
Funded by
NIH| A Unified Atlas of Dynamic tRNA Function
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2R01HG006753-04A1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

Lowe, T.M., Eddy, S.R.. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res.. 1997; 25: 955-964 [OpenAIRE] [PubMed]

Chan, P.P., Lowe, T.M.. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res.. 2009; 37: D93-D97 [OpenAIRE] [PubMed]

Chan, P.P., Lowe, T.M.. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res.. 2016; 44: D184-D189 [OpenAIRE] [PubMed]

Schattner, P., Brooks, A.N., Lowe, T.M.. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res.. 2005; 33: W686-W689 [OpenAIRE] [PubMed]

Nawrocki, E.P., Eddy, S.R.. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013; 29: 2933-2935 [OpenAIRE] [PubMed]

Giege, R., Sissler, M., Florentz, C.. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res.. 1998; 26: 5017-5035 [OpenAIRE] [PubMed]

Perry, J., Dai, X., Zhao, Y.. A mutation in the anticodon of a single tRNAala is sufficient to confer auxin resistance in Arabidopsis. Plant Physiol.. 2005; 139: 1284-1290 [OpenAIRE] [PubMed]

Kimata, Y., Yanagida, M.. Suppression of a mitotic mutant by tRNA-Ala anticodon mutations that produce a dominant defect in late mitosis. J. Cell Sci.. 2004; 117: 2283-2293 [OpenAIRE] [PubMed]

Ardell, D.H., Andersson, S.G.. TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. Nucleic Acids Res.. 2006; 34: 893-904 [OpenAIRE] [PubMed]

Speir, M.L., Zweig, A.S., Rosenbloom, K.R., Raney, B.J., Paten, B., Nejad, P., Lee, B.T., Learned, K., Karolchik, D., Hinrichs, A.S.. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res.. 2016; 44: D717-D725 [OpenAIRE] [PubMed]

Chan, P.P., Holmes, A.D., Smith, A.M., Tran, D., Lowe, T.M.. The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res.. 2012; 40: D646-D652 [OpenAIRE] [PubMed]

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 lin...
Subjects
free text keywords: Genome, Molecular biology, Genetics, Biology, Genome project, Gene, RNA, Web server, computer.software_genre, computer, DNA sequencing, Transfer RNA, Annotation, Web Server issue
Funded by
NIH| A Unified Atlas of Dynamic tRNA Function
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2R01HG006753-04A1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

Lowe, T.M., Eddy, S.R.. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res.. 1997; 25: 955-964 [OpenAIRE] [PubMed]

Chan, P.P., Lowe, T.M.. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res.. 2009; 37: D93-D97 [OpenAIRE] [PubMed]

Chan, P.P., Lowe, T.M.. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res.. 2016; 44: D184-D189 [OpenAIRE] [PubMed]

Schattner, P., Brooks, A.N., Lowe, T.M.. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res.. 2005; 33: W686-W689 [OpenAIRE] [PubMed]

Nawrocki, E.P., Eddy, S.R.. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013; 29: 2933-2935 [OpenAIRE] [PubMed]

Giege, R., Sissler, M., Florentz, C.. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res.. 1998; 26: 5017-5035 [OpenAIRE] [PubMed]

Perry, J., Dai, X., Zhao, Y.. A mutation in the anticodon of a single tRNAala is sufficient to confer auxin resistance in Arabidopsis. Plant Physiol.. 2005; 139: 1284-1290 [OpenAIRE] [PubMed]

Kimata, Y., Yanagida, M.. Suppression of a mitotic mutant by tRNA-Ala anticodon mutations that produce a dominant defect in late mitosis. J. Cell Sci.. 2004; 117: 2283-2293 [OpenAIRE] [PubMed]

Ardell, D.H., Andersson, S.G.. TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. Nucleic Acids Res.. 2006; 34: 893-904 [OpenAIRE] [PubMed]

Speir, M.L., Zweig, A.S., Rosenbloom, K.R., Raney, B.J., Paten, B., Nejad, P., Lee, B.T., Learned, K., Karolchik, D., Hinrichs, A.S.. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res.. 2016; 44: D717-D725 [OpenAIRE] [PubMed]

Chan, P.P., Holmes, A.D., Smith, A.M., Tran, D., Lowe, T.M.. The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res.. 2012; 40: D646-D652 [OpenAIRE] [PubMed]

Powered by OpenAIRE Open Research Graph
Any information missing or wrong?Report an Issue
publication . Other literature type . Article . 2016

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

Todd M Lowe; Patricia P Chan;