gtrnadb.ucsc.edu
GtRNAdb: Genomic tRNA DatabaseGenomic tRNA database 2.0
http://gtrnadb.ucsc.edu/
Genomic tRNA database 2.0
http://gtrnadb.ucsc.edu/
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GtRNAdb: Genomic tRNA Database | gtrnadb.ucsc.edu Reviews
https://gtrnadb.ucsc.edu
Genomic tRNA database 2.0
gtrnadb.ucsc.edu
GtRNAdb: Genomic tRNA Database
http://gtrnadb.ucsc.edu/blast.html
Search by Seqeunce Using BLAST. Alignment Program - blastn: nucleotide query vs. nucleotide db. Formatted (FASTA, GenBank). OR Load query from file:. Biomolecular Engineering, University of California Santa Cruz.
GtRNAdb: Genomic tRNA Database
http://gtrnadb.ucsc.edu/legend.html
Each new tRNA in a sequence is consecutively numbered in the "tRNA #" column. "tRNA Bounds" specify the starting (5') and ending (3') nucleotide bounds for the tRNA. tRNAs found on the reverse (lower) strand are indicated by having the Begin (5') bound greater than the End (3') bound (see tRNAs #4 and #5 in output above). TRNA with Anticodon CAT. The current version of tRNAscan-SE does not include the analysis of identifying between initiator tRNA-Met, elongator tRNA-Met, and tRNA-Ile with anticodon CAT&...
GtRNAdb: Genomic tRNA Database
http://gtrnadb.ucsc.edu/faq.html
I downloaded tRNAscan-SE to look for tRNAs in my genome. Why do I get a lot more tRNA predictions than those included in GtRNAdb? TRNA-derived repetitive elements, whose primary sequences are very similar to real tRNA genes, have been commonly found in a lot of vertebrates, some worms, and some plants. We plan to add a new feature to identify this specific type of element within tRNAscan-SE, although the current version does not effectively discriminate between atypical tRNAs and tRNA-derived SINEs.
GtRNAdb: Genomic tRNA Database
http://gtrnadb.ucsc.edu/other-links.html
Other Links of Interest. Modomics - a database of RNA modification pathways. TRFdb - a relational database of tRNA related fragments. Rfam - RNA families database of alignments and CMs. TRNA family (RF00005) in Rfam. The RNA World @ IMB Jena. JGI Integrated Microbial Genomes. Biomolecular Engineering, University of California Santa Cruz.
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The Lowe Lab - Tools and Databases
http://lowelab.ucsc.edu/databases.html
UCSC Archaeal Genome Browser. TRNA alignments in GtRNAdb. TRNAscan-SE for tRNA predictions ( http:/ lowelab.ucsc.edu/tRNAscan-SE/. Snoscan for C/D box snoRNA predictions ( http:/ lowelab.ucsc.edu/snoscan/. SnoGPS for H/ACA snoRNA predictions ( http:/ lowelab.ucsc.edu/snoGPS/. UCSC Archaeal Genome Browser ( http:/ archaea.ucsc.edu. UCSC Microbial Genome Browser ( http:/ microbes.ucsc.edu. Genomic tRNA Database ( http:/ gtrnadb.ucsc.edu.
genomeinformatician.blogspot.com
Ewan's Blog: Bioinformatician at large: October 2014
http://genomeinformatician.blogspot.com/2014_10_01_archive.html
Ewan's Blog: Bioinformatician at large. Tuesday, 28 October 2014. RNA is now a first class bioinformatics molecule. RNA research is expanding very quickly, and a public resource for these extremely valuable datasets has been long overdue. And then there are long RNAs in mammalian genomes that do not encode proteins (i.e. long non-coding RNA - lincRNA) have long been recognised as having some significance – but what do they do? For miRNAs, or Todd Lowe’s gtRNAdb. Resource from for tRNAs. But because R...
The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis | The EMBO Journal
http://emboj.embopress.org/content/early/2015/08/13/embj.201591382
Skip to main content. The EMBO Journal (Home). Search for this keyword. Review Series and Focuses. The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis. Published online 13.08.2015. German Cancer Research Center. Find this author on Google Scholar. Find this author on PubMed. Search for this author on this site. Department of Translational Oncology. National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ). Find this author on PubMed.
Hou Laboratory
http://www.houlaboratory.org/links
Dept of Biochemistry and Molecular biology. Thomas Jefferson University homepage. Pedro's Molecular Biology page. Stem ExPASy Proteomics Server. J Craig Venter Institute. Aminoacyl-tRNA Synthetases Databank Sequences of most known tRNA synthetases, plus additional information on tRNA. Pubmed for Medline, BLAST and Genbank searches. Genomic tRNA database tRNAscan-SE analysis of complete genomes. TRNA Gene DataBase Curated by Experts. Mammalian mitochondrial tRNA database. Protein Data bank (at RCSB).
gtRNAdb Expert Database
http://www.rnacentral.org/expert-database/gtrnadb
Your query is too short. Your query is too long. Contains tRNA gene predictions on complete or nearly complete genomes. Distinct sequences from 382. Organisms contributed to RNAcentral. The shortest sequence has 65. Nucleotides, the longest 128. The average length is 77. Browse all gtRNAdb sequences. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Chan P.P., Lowe T.M. Nucleic Acids Res. 37(Database issue):D93-D97(2009). Click the graph to search by sequence length. Result.entr...
Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation
http://aem.asm.org/content/78/4/1015.full
American Society for Microbiology. Applied and Environmental Microbiology. Skip to main page content. Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation. Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan. Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan. Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan. And typica...
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GtRNAdb: Genomic tRNA Database
TRNAscan-SE analysis of complete genomes. The genomic tRNA database contains tRNA gene predictions made by tRNAscan-SE. On complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature. To access the previous version of GtRNAdb that includes gene predictions using the stable version of tRNAscan-SE 1.23 and 1.3, please click here. Links to Most Viewed Genomes. Str K-12 substr. MG1655. BDGP Rel. 6/dm6).
Genomic tRNA Database
This genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE ( Lowe and Eddy, Nucl Acids Res. On complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature. Inevitably with automated sequence analysis, we find exceptions to general identification rules, isoacceptor type predictions ( esp. Pristionchus pacificus (WUGSC 5.0 Feb 2007). Brachypodium distachyon (JGI v1.0 8X). Caenorha...
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