pppBenchmark A large-scale benchmarking study of 17 state-of-the-art Promoter Prediction Programs
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pppBenchmark Tags

prediction emotional state prediction webpage promoter promoter site promoter large scale deployments gene website promoter gene annotation ad promoter Island Promoter Detection Extract Promoter Promoter Extraction promoter extractor study bound state systems Large-scale Analysis large-scale

pppBenchmark Description

A multi-faceted evaluation strategy is proposed that can be used as a gold standard for promoter prediction evaluation, allowing authors of promoter prediction software to compare their method to existing methods in a proper way. This evaluation strategy is subsequently used to compare the chosen promoter predictors, and an in-depth analysis on predictive performance, promoter class specificity, overlap between predictors and positional bias of the predictions is conducted. When using this program to validate newly developed programs, it is important that you don't use the data that is used for validation in pppBenchmark as training data for your program. The proper procedure here would be to split the data in training and testing, and run your program and pppBenchmark for each split. The best way to split the data is on the level of complete chromosomes. For example use 23 chromosomes for training and the one left out for validation. Do this for each chromosome left out. Get pppBenchmark and give it a try to see just how useful it can actually be for you!

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