With the availability of prediction methods for all major steps of the HLA class I processing pathway, it became possible to model the whole pathway.
While the availability of predictions is low (9%), we note first that many of the 2935 proteins are likely to be non-enzymes, for which the lack of enzymatic activity prediction is a desirable outcome.
Availability: Predictions for the human genome, the validation datasets and the program (ProSOM) are available upon request.
In order to address the effect on the loss of coding efficiency when using FMO because of the reduced availability of MBs for intermotion prediction, we adapt the model in (1) to model the header bits of P-frames.
Hence, experiments with different values of this parameter allow us to study the aforementioned trade-off between statistical reliability and availability of relevant attributes for prediction.
The usefulness depends on the availability of alternative strategies for disease prediction and the availability of preventive or therapeutic interventions that can be targeted to genetic profiles, among other factors, such as effectiveness and cost-effectiveness of interventions, and patient preferences and attitudes.
The idea to model antigen presentation in detail is motivated by the availability of parameters for these processes, including, for example, in silico T-epitope prediction and experimental measurements of their MHC-binding affinities.
A fourth prediction derives from the availability of one label for incremental grouping.
Thus, further testing of our predictions will be necessary upon availability of better estimates for the crowding coefficients.
Authors' response: Limited by the current availability of data, especially for golden standard PPI datasets available for verification, we use indirect approaches to assess the performance of our prediction approach.
