PsRobot: a web-based plant small RNA meta-analysis toolbox.
Small RNAs (smRNAs) in plants, mainly microRNAs and small interfering RNAs, play important roles in both transcriptional and post-transcriptional gene regulation. The broad application of high-throughput sequencing technology has made routinely generation of bulk smRNA sequences in laboratories possible, thus has significantly increased the need for batch analysis tools. PsRobot is a web-based easy-to-use tool dedicated to the identification of smRNAs with stem-loop shaped precursors (such as microRNAs and short hairpin RNAs) and their target genes/transcripts. It performs fast analysis to identify smRNAs with stem-loop shaped precursors among batch input data and predicts their targets using a modified Smith-Waterman algorithm. PsRobot integrates the expression data of smRNAs in major plant smRNA biogenesis gene mutants and smRNA-associated protein complexes to give clues to the smRNA generation and functional processes. Besides improved specificity, the reliability of smRNA target prediction results can also be evaluated by mRNA cleavage (degradome) data. The cross species conservation statuses and the multiplicity of smRNA target sites are also provided. PsRobot is freely accessible at http://omicslab.genetics.ac.cn/psRobot/.
The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Hua-Jun
HJ
Wu
Ying-Ke
YK
Ma
Tong
T
Chen
Meng
M
Wang
Xiu-Jie
XJ
Wang
D000465:Algorithms; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism; D012322:RNA Precursors / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
D035683:MicroRNAs; D012322:RNA Precursors; D012333:RNA, Messenger; D018749:RNA, Plant; D058727:RNA, Small Untranslated