Impact of RNA structure on the prediction of donor and acceptor splice sites. BMC Bioinformatics. 2006; 7 (1):297. doi: 10.1186/1471-2105-7-297. [ Cross Ref ]Marashi S.A., Eslahchi C., Pezeshk H. et al. (2006) Impact of RNA structure on the prediction of donor and acceptor ...
SpTransformer is a computational model that predicts the probability of each position in a pre-mRNA input sequence being a splice donor, splice acceptor, or neither in all and 15 different tissues simultaneously (Fig. 1a). Previous studies have demonstrated the effectiveness of deep convolutional ne...
The final fully connected layer has three neurons which correspond to acceptor site, donor site, and non-splice-site. Softmax activation function [27] is used for the neurons in the last fully connected layer to convert the output into normalized probability. For training, cross-entropy [28] ...
The SS at the exon/intron boundary corresponds to the donor site (DoSS), while the SS at the intron/exon boundary is the acceptor site (AcSS). The DoSS and AcSS are characterized in most cases by canonical GT and AG dinucleotides in DNA (Burset et al., 2000), respectively. In silico...
SpTransformer is a computational model that predicts the probability of each position in a pre-mRNA input sequence being a splice donor, splice acceptor, or neither in all and 15 different tissues simultaneously (Fig. 1a). Previous studies have demonstrated the effectiveness of deep convolutional ne...
non-coding regions (introns). Splice site is the general term for the point at the beginning (donor site) or at the end (acceptor site) of an intron. Donor and acceptor sites typically correspond to certain patterns, but the same patterns can also be found in other places in the DNA ...
So, we combined the false donor and acceptor groups, and after preprocessing, our final dataset had three classes: true donor, true acceptor, and non-site. There were 2796 sequences in the true donor class and 2880 sequences in the true acceptor class; therefore, the true donor and true ...
These include the poly(A) site, the major splice donor site and the splice acceptor sites. The inherent efficiency of the HIV-1 poly(A) site allows maximal activity where there is no donor site (in the 3' LTR) but full inhibition by the downstream MSD (in the 5' LTR). The MSD ...
0= Donor site 1= Acceptor site 2= Negative example (non-splice site region) transcript: This column contains detailed transcript information, including the identifier for the transcript and potentially the chromosome number. The sequences themselves are extracted from FASTA files based on the coordina...
We did not removed cross-correlation between the learning set and the test set of 183 rat genes. Figure 3 Bayesian sensor histograms produced for 5' SS and 3' SS signals on the test set of 250 human genes. Full size image Figure 4 ROC diagrams for Donor and Acceptor signals. Full size...