iPromoter-2L2.0: Identifying Promoters and Their Types by Combining Smoothing Cutting Window Algorithm and Sequence-Based Features

Promoters are short regions at specific locations of DNA sequences, which are playing key roles in directing gene transcription. They can be grouped into six types ([Formula: see text]). Recently, a predictor called “iPromoter-2L” was constructed to predict the promoters and their six types, which is the first approach to predict all the six types of promoters. However, its predictive quality still needs to be further improved for real-world application requirement. In this study, we proposed the smoothing cutting window algorithm to find the window fragments of the DNA sequences based on the conservation scores to capture the sequence patterns of promoters. For each window fragment, the discriminative features were extracted by using kmer and PseKNC. Combined with support vector machines (SVMs), different predictors were constructed and then clustered into several groups based on their distances. Finally, a new predictor called iPromoter-2L2.0 was constructed to identify the promoters and their six types, which was developed by ensemble learning based on the key predictors selected from the cluster groups. The results showed that iPromoter-2L2.0 outperformed other existing methods for both promoter prediction and identification of their six types, indicating that iPromoter-2L2.0 will be helpful for genomics analysis.