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Bioinformatics. 2014 Apr 1;30(7):1045-6. doi: 10.1093/bioinformatics/btt746. Epub 2013 Dec 25.

tasiRNAdb: a database of ta-siRNA regulatory pathways.

Author information

1
College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China, College of Forest Resources and Environment, Nanjing Forestry University, Nanjing 210037, China and College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.

Abstract

SUMMARY:

In plants, many trans-acting small interfering RNA (ta-siRNA) regulatory pathways have been identified as significant components of the gene networks involved in development, metabolism, responses to biotic and abiotic stresses and DNA methylation at the TAS locus. To obtain a more comprehensive understanding on the nature of ta-siRNA regulatory pathways, we developed a freely accessible resource, tasiRNAdb, to serve as a repository for the sequences of ta-siRNA regulatory pathway-related microRNAs, TASs, ta-siRNAs and ta-siRNA targets, and for the cascading relations among them. With 583 pathways from 18 species, tasiRNAdb is the largest resource for known ta-siRNA regulatory pathways currently available. tasiRNAdb also provides a tool named TasExpAnalysis that was developed to map user-submitted small RNA and degradome libraries to a stored/input TAS and to perform sRNA phasing analysis and TAS cleavage analysis.

AVAILABILITY:

The database of plant ta-siRNA regulatory pathways is available at http://bioinfo.jit.edu.cn/tasiRNADatabase/.

PMID:
24371150
DOI:
10.1093/bioinformatics/btt746
[Indexed for MEDLINE]

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