tRFdb: a database for transfer RNA fragments | Zendy

Pankaj Kumar | Zendy; Suresh B. Mudunuri | Zendy; Jordan Anaya | Zendy; Anindya Dutta | Zendy

AI Assistant Blog Pricing

Home ZAIA Blog

Open Access

tRFdb: a database for transfer RNA fragments

Author(s) -

Pankaj Kumar,

Suresh B. Mudunuri,

Jordan Anaya,

Anindya Dutta

Publication year - 2014

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gku1138

Subject(s) - biology , transfer rna , genome , rna , database , genetics , sequence (biology) , computational biology , sequence database , rna editing , non coding rna , gene , computer science

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.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research