MTide

[…] engine and the rna-hybrid search engine, respectively. moreover, several integrated bioinformatics tools and software have been developed to identify and predict mirnas and their targets (). taking mtide for example, the combination of a modified mirdeep2 , a modified cleaveland4 , and some other useful scripts is used to calculate expression profiles of known mirs, predict novel mirnas, […]

[…] were used for the prediction of novel mirnas using mireap (http://sourceforge.net/projects/mireap/), a software developed by bgi. also, both dnaman 8 (http://www.lynnon.com/pc/framepc.html) and mtide (http://bis.zju.edu.cn/mtide) [] were used for the prediction of novel mirnas. only these mirna candidates being simultaneously predicted by the three softwares were regarded to be novel […]

[…] generation of new mirnas. these phenomena are consistent with previous reports on the mirnas of both plants and animals., the remaining non-annotated sequences (538,928 reads; ) were assigned using mtide software (http://bis.zju.edu.cn/mtide/) for novel mirna prediction. finally, 312 candidate novel mirnas were identified, and their characteristic hairpin structure formation ability […]

[…] of mirna and mirna* (16), maximal bulge of mirna and mirna* (4), maximal asymmetry of mirna/mirna* duplex (4) and flank sequence length of mirna precursor (20; lu et al., ). in addition, we used mtide (http://bis.zju.edu.cn/mtide; zhang et al., ) and dnaman 8 (http://www.lynnon.com/pc/framepc.html) to predict novel mirna. only these mirna candidates that were simultaneously predicted […]

[…] by the bgi, by exploring the secondary structure, the dicer cleavage site and the minimum free energy of the unannotated small rna tags which could be mapped to genome. in addition, we used mtide: an integrated tool for the identification of mirna-target interaction in plants (http://bis.zju.edu.cn/mtide) [] and dnaman 8 (http://www.lynnon.com/pc/framepc.html) to predict novel mirna. […]