TRNADB

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tRNAdb
Content
Descriptioncompilation of tRNA sequences and tRNA genes
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LaboratoryUniversities of Leipzig, Marburg, and Strasbourg
Primary citationJuhling et al. (2009) [1]
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Website Website

tRNAdb was a comprehensive biological database of transfer RNA (tRNA) sequences and tRNA genes. It originated as one of the first specialized compilations of nucleic acid sequences, starting as a print publication by Mathias Sprinzl in the late 1970s. [2] It evolved into a web-based resource hosted at the University of Bayreuth and was later relaunched in 2009 as a more powerful relational database at the University of Leipzig. [1] The database is now considered defunct, as the Leipzig-based resource is no longer active. Its role has largely been superseded by other modern tRNA databases.

Contents

tRNADB-CE

The tRNA Gene Database Curated by Experts (tRNADB-CE) is a database of tRNA genes developed and maintained by researchers at Niigata University and the Nagahama Institute of Bio-Science and Technology in Japan. A key feature of tRNADB-CE is its rigorous curation process. It uses three different tRNA gene prediction programs (tRNAscan-SE, ARAGORN, and tRNAfinder) and identifies any discordant results. These conflicting predictions are then manually reviewed by experts to ensure high accuracy. [3] [4]

GtRNAdb

The Genomic tRNA Database (GtRNAdb) is a database of tRNA genes found in complete and draft genomes. Hosted at the University of California, Santa Cruz (UCSC) and maintained by the laboratory of Todd Lowe, GtRNAdb is built using predictions from a single, highly accurate software tool, tRNAscan-SE. [5] It provides detailed information on genomic location, isotype, and secondary structure, and it is tightly integrated with the UCSC Genome Browser. Its focus is on providing high-quality, automated annotations of tRNA genes across all domains of life. [6]

See also

References

  1. 1 2 Jühling, F; Mörl, M; Hartmann, RK; Sprinzl, M; Stadler, PF; Pütz, J (1 January 2009). "tRNAdb 2009: compilation of tRNA sequences and tRNA genes". Nucleic Acids Research. 37 (Database issue): D159 –D162. doi:10.1093/nar/gkn772. PMC   2686557 . PMID   18957446.
  2. ↑ Sprinzl, M. (December 17, 2004). "Compilation of tRNA sequences and sequences of tRNA genes" (PDF). Nucleic Acids Research. 33 (Database issue). Oxford University Press (OUP): D139 –D140. doi: 10.1093/nar/gki012 . ISSN   1362-4962. PMC   539966 . PMID   15608164 . Retrieved July 15, 2025.
  3. ↑ Abe, Takashi; Ikemura, Toshimichi; Ohara, Yasuo; Uehara, Hiroshi; Kinouchi, Makoto; Kanaya, Shigehiko; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro (October 8, 2008). "tRNADB-CE: tRNA gene database curated manually by experts". Nucleic Acids Research. 37 (suppl_1). Oxford University Press (OUP): D163 –D168. doi: 10.1093/nar/gkn692 . ISSN   1362-4962. PMC   2686568 . PMID   18842632.
  4. ↑ Abe, T.; Ikemura, T.; Sugahara, J.; Kanai, A.; Ohara, Y.; Uehara, H.; Kinouchi, M.; Kanaya, S.; Yamada, Y.; Muto, A.; Inokuchi, H. (November 11, 2010). "tRNADB-CE 2011: tRNA gene database curated manually by experts" (PDF). Nucleic Acids Research. 39 (Database). Oxford University Press (OUP): D210 –D213. doi: 10.1093/nar/gkq1007 . ISSN   0305-1048. PMID   21071414 . Retrieved July 15, 2025.
  5. ↑ Chan, PP; Lowe, TM (January 2009). "GtRNAdb: a database of transfer RNA genes detected in genomic sequence". Nucleic Acids Research. 37 (Database issue): D93 –D97. doi:10.1093/nar/gkn787. PMC   2686519 . PMID   18984615.
  6. ↑ Chan, Patricia P.; Lowe, Todd M. (December 15, 2015). "GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes" (PDF). Nucleic Acids Research. 44 (D1). Oxford University Press (OUP): D184 –D189. doi: 10.1093/nar/gkv1309 . ISSN   0305-1048. PMC   4702915 . PMID   26673694 . Retrieved July 15, 2025.
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