Terminator prediction

The following interface serves as a visualization of the results produced by TSS-CAPTUR. The possibility exists between an overview of all results or the detailed results of the classification or the terminator allocation steps of TSS-CAPTUR. The possibility of some TSS being ignored by TSS-CAPTUR due to their short length exists. They are found here. For the more information on the tools and parameters used in TSS-CAPTUR, please refer to the references.

The current page presents a detailed view on the results of the terminator allocation for RNA transcripts. TSS-CAPTUR predicts intrinsic as well as rho-dependent terminators using TransTermHP and RhoTermPredict, respectively. QRNA and CNIT already provide the coordinates of the most probable functional subsequence. If a terminator is found within these coordinates, the terminator is allocated to the corresponding transcript. The terminator is evaluated wrt. to the predicted coordinates of the classification to ensure a terminator close to the 3' end of the predicted gene. If many terminators are allocated to the same TSS, only the best-scored terminator is chosen. If this terminator is classified as rho-dependent, an intrinsic terminator is search within a window of 150 nts. If a terminator is allocated to many TSSs, the terminators are ranked wrt. to the TSS and the computed score. The 3'-end coordinates of only those transcripts with the best-ranked terminators are updated.