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PtRFdb: a database for plant transfer RNA-derived fragments

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Title PtRFdb: a database for plant transfer RNA-derived fragments
 
Creator Gupta, Nikita
Singh, Ajeet
Zahra, Shafaque
Kumar, Shailesh
 
Subject database
PtRFdb
plant transfer RNA-derived fragments
 
Description Accepted date: 29 May 2018
Transfer RNA-derived fragments (tRFs) represent a novel class of small RNAs (sRNAs) generated through endonucleolytic cleavage of both mature and precursor transfer RNAs (tRNAs). These 14–28 nt length tRFs that have been extensively studied in animal kingdom are to be explored in plants. In this study, we introduce a database of plant tRFs named PtRFdb (www.nipgr.res.in/PtRFdb), for the scientific community. We analyzed a total of 1344 sRNA sequencing datasets of 10 different plant species and identified a total of 5607 unique tRFs (758 tRF-1, 2269 tRF-3 and 2580 tRF-5), represented by 487 765 entries. In PtRFdb, detailed and comprehensive information is available for each tRF entry. Apart from the core information consisting of the tRF type, anticodon, source organism, tissue, sequence and the genomic location; additional information like PubMed identifier (PMID), Sample accession number (GSM), sequence length and frequency relevant to the tRFs may be of high utility to the user. Two different types of search modules (Basic Search and Advanced Search), sequence similarity search (by BLAST) and Browse option with data download facility for each search is provided in this database. We believe that PtRFdb is a unique database of its kind and it will be beneficial in the validation and further characterization of plant tRFs.

Database URL: http://www.nipgr.res.in/PtRFdb/
This work was supported by core research grant from National
Institute of Plant Genome Research (NIPGR), India, an autonomous
institute of Department of Biotechnology (DBT), India.
 
Date 2018-06-26T04:51:47Z
2018-06-26T04:51:47Z
2018
 
Type Article
 
Identifier Database, 2018: bay063
1758-0463
http://223.31.159.10:8080/jspui/handle/123456789/866
https://academic.oup.com/database/article/doi/10.1093/database/bay063/5043071
https://doi.org/10.1093/database/bay063
 
Language en_US
 
Format application/pdf
 
Publisher Oxford University Press