Background: Trans-action siRNA (ta-siRNA) is a type of small interfering RNA detected from plant and is reported to play an important role in post transcriptional regulation.Previously studies demonstrated that ta-siRNA is produced by microRNA-directed mRNA degradation.A genomic panorama of this new RNA and the understanding of its molecule mechanism in gene regulation depends on the development of efficient strategy to recognize ta-siRNA.Methods: According to the phased feature of ta-siRNA genes (TAS), we first check if the small RNAs detected from high-throughput sequencing tend to locate at phased site in a small RNA cluster.Then we seek miRNAs that could target at this cluster, which would potentially initiate the synthesis of ta-siRNAs.Degradome data is introduced to verify the cleavage directed by microRNA.By further predicting the targets of identified ta-siRNA, a tasiRNA regulatory cascade could be inferred.Results: We proposed a new tool, TasiAyser, to find ta-siRNAs and the target of tasiRNAs, which employed the features of ta-siRNA and the degradome sequencing data.Using high-throughput sequencing data download from GEO (GSM643815) and degradome data (GSM643817), TasiAyser report 13 TASs and 6 regulation pathways from Medicago truncatula.Nine of the predicted TASs, including a TAS that is conserved between Arabidopsis and Medicago, have been mentioned by previous studies.TasiAyser is available on the web site: http://mcube.nju.edu.cn/jwang/lab/soft/TasiAyser/ Conclusions: TasiAyser shows a high accuracy and specificity by employing the newly detected features of ta-siRNAs and the degradome data.In the case of Medicago truncatula, TasiAyser identified several new TASs, including a conserved TAS between Arabidopsis and Medicago .