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Nucleic Acids Res. 2015 Jan;43(Database issue):D141-5. doi: 10.1093/nar/gku1138. Epub 2014 Nov 11.

tRFdb: a database for transfer RNA fragments.

Author information

1
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
2
Department of Computer Science and Engineering, Grandhi Varalakshmi Venkatarao Institute of Technology (GVIT), Bhimavaram, Andhra Pradesh 534207, India.
3
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA ad8q@virginia.edu.

Abstract

We have created tRFdb, the first database of transfer RNA fragments (tRFs), available at http://genome.bioch.virginia.edu/trfdb/. With over 100 small RNA libraries analyzed, the database currently contains the sequences and read counts of the three classes of tRFs for eight species: R. sphaeroides, S. pombe, D. melanogaster, C. elegans, Xenopus, zebra fish, mouse and human, for a total of 12,877 tRFs. The database can be searched by tRF ID or tRF sequence, and the results can be limited by organism. The search results show the genome coordinates and names of the tRNAs the sequence may derive from, and there are links for the sequence of the tRF and parental tRNA, and links for the read counts in all the corresponding small RNA libraries. As a case study for how this database may be used, we have shown that a certain class of tRFs, tRF-1s, is highly upregulated in B-cell malignancies.

PMID:
25392422
PMCID:
PMC4383946
DOI:
10.1093/nar/gku1138
[Indexed for MEDLINE]
Free PMC Article

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