tRFdb: a database for transfer RNA fragments.
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.
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
Pankaj
P
Kumar
Department of Computer Science and Engineering, Grandhi Varalakshmi Venkatarao Institute of Technology (GVIT), Bhimavaram, Andhra Pradesh 534207, India.
Suresh B
SB
Mudunuri
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
Jordan
J
Anaya
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA ad8q@virginia.edu.
Anindya
A
Dutta
D000818:Animals; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D016393:Lymphoma, B-Cell / Q000235:genetics; D051379:Mice; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
D012343:RNA, Transfer