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PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs

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Title PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs
 
Creator Gupta, Nikita
Zahra, Shafaque
Singh, Ajeet
Kumar, Shailesh
 
Subject database
plant exclusive virus-derived small interfering RNAs
PVsiRNAdb
Ribonucleic acids (RNA)
Database tool
 
Description Accepted date: 14 September 2018
Ribonucleic acids (RNA) interference mechanism has been proved to be an important
regulator of both transcriptional and post-transcription controls of gene expression
during biotic and abiotic stresses in plants. Virus-derived small interfering RNAs
(vsiRNAs) are established components of the RNA silencing mechanism for incurring
anti-viral resistance in plants. Some databases like siRNAdb, HIVsirDB and VIRsiRNAdb
are available online pertaining to siRNAs as well as vsiRNAs generated during viral
infection in humans; however, currently there is a lack of repository for plant exclusive
vsiRNAs. We have developed ‘PVsiRNAdb (http://www.nipgr.res.in/PVsiRNAdb)’, a
manually curated plant-exclusive database harboring information related to vsiRNAs
found in different virus-infected plants collected by exhaustive data mining of published
literature so far. This database contains a total of 322 214 entries and 282 549 unique
sequences of vsiRNAs. In PVsiRNAdb, detailed and comprehensive information is
available for each vsiRNA sequence. Apart from the core information consisting of plant,
tissue, virus name and vsiRNA sequence, additional information of each vsiRNAs (map
position, length, coordinates, strand information and predicted structure) may be of
high utility to the user. Different types of search and browse modules with three different
tools namely BLAST, Smith–Waterman Align and Mapping are provided at PVsiRNAdb.
Thus, this database being one of its kind will surely be of much use to molecular
biologists for exploring the complex viral genetics and genomics, viral–host interactions
and beneficial to the scientific community and can prove to be very advantageous in the
field of agriculture for producing viral resistance transgenic crops.
Database URL: http://www.nipgr.res.in/PVsiRNAdb
The authors are thankful to Department of Biotechnology (DBT)-eLibrary Consortium, India, for providing access to e-resources and to DBT Distributed Information Sub-Centre Facility at National Institute of Plant Genome Research. S.Z. and A.S. are thankful to Council of Scientific and Industrial Research, India, for their research fellowships. The authors are also thankful to Shahre Aalam for the help in the literature search. The authors declare no competing financial interests. This work was supported by core research grant from the National Institute of Plant Genome Research (NIPGR), India, an autonomous institute of Department of Biotechnology (DBT), India. Database URL:http://www.nipgr.res.in/PVsiRNAdb
 
Date 2018-10-22T10:05:12Z
2018-10-22T10:05:12Z
2018
 
Type Article
 
Identifier Database, 2018: bay105
1758-0463
http://223.31.159.10:8080/jspui/handle/123456789/890
https://academic.oup.com/database/article/doi/10.1093/database/bay105/5126495
https://doi.org/10.1093/database/bay105
 
Language en_US
 
Format application/pdf
 
Publisher Oxford University Press