Results were stored in a MySQL database and a web interface was prepared to query the database and retrieve predictions of interest.
In the near future, PredictProtein (Rost et al., 2004) that provides the framework for SNAP, will store sequences and retrieve predictions for additional mutants in real time.
24 To evaluate the predictive performance of the retrieved prediction models, we used the original prediction models (regression coefficients with intercept or baseline hazard) as published.
The retrieved prediction models differed considerably in terms of type and number of predictors, age ranges, type of model, duration of follow-up, and outcome measure.
We retrieved prediction accuracy data for more than 550,000 SNPs for 14 climate, subsistence, and pathogen-related environmental factors that were used in Fumagalli et al. (2011).
Detailed method for retrieving prediction and score from these applications is described in Additional file 1: Method B. EFIN, MutationTaster, PhyloP, GERP++ and SIFT were tested on Swiss-Prot dataset.
Finally, we retrieve the prediction results from the URI shown in Appendix 4. The prediction results (Appendix 5) are represented as ot:Dataset (e.g. table with variable number of columns), which consists of data entries (ot:DataEntry) relating compounds (e.g. rows) to features (columns, ot:Feature).
This in turn requires systems that allow researchers to quickly retrieve model predictions for visualization and analysis.
All predicted ORFs were then submitted to local RPS-BLAST [ 33] and the NCBI CDD database to retrieve domain predictions with an e-value < 10-5.
Comparing distributions of hits in GO classes from the two sets of statistics allows to highlight over- or under-targeted categories, and to retrieve corresponding predictions.
