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To remedy these problems, we focused on a limited set of MHC class II alleles for which good predictions exist, and selected those available in the TEPITOPE method [81].
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This in turn can both help identify co-regulators for which only computational predictions exists and also lead to the identification of different waves of transcriptional regulation, where the same TFs activate different sets of genes at different time points.
Where multiple predictions existed around a single locus (2000 base pairs), only the prediction with the highest score was kept.
For applications in chemical engineering, where requirements for accurate vapor pressure correlations and predictions exist, the results from transferable force fields are sometimes insufficient.
For PLCγ1 and RasGAP (N-terminal SH2) opposing predictions exist [31], [41].
Second, we consider the average duration of reactive trajectories for which no theoretical predictions exist.
MiRABELLE takes as input an expression dataset and produces a miR-seed activity matrix, giving for each sample in the dataset, the activity scores computed for each of the miRNA species for which predictions exist.
Finally, Ensembl chimpanzee gene predictions exist for 14 of the genes from cluster 19.12 given as missing or defective in Tadepally et al. [ 2].
High throughput proteomics experiments (mass spectrometry) provide unique insight into the protein expression profile of an organism and can be useful in identifying the correct gene structure of a genome, particularly when splice variants or alternative gene predictions exist, or to elucidate the roles of post-translational modifications within proteins [ 1].
Model performance analysis was conducted on the initial NN model to find if weak prediction regions exist, and further rolling data to cover these weak regions were generated and the extended data were used for re-training.
Many other ab initio gene prediction algorithms exist and these are reviewed by Do and Choi [ 14].
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