Abstract Motivation Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types. Promoters may have both intra and inter class variation and similarity in terms of consensus sequences. Accurate classification of various types of sigma promoters still remains a challenge. Results We present iPromoter-BnCNN for identification and accurate classification of six types of promoters - σ24, σ28, σ32, σ38, σ54, σ70. It is a CNN based classifier which combines local features related to monomer nucleotide sequence, trimer nucleotide sequence, dimer structural properties and trimer structural properties through the use of parallel branching. We conducted experiments on a benchmark dataset and compared with six state-of-the-art tools to show our supremacy on 5-fold cross-validation. Moreover, we tested our classifier on an independent test dataset. Availability Our proposed tool iPromoter-BnCNN web server is freely available at http://103.109.52.8/iPromoter-BnCNN. The runnable source code can be found https://colab.research.google.com/drive/1yWWh7BXhsm8U4PODgPqlQRy23QGjF2DZ Supplementary information Supplementary data (benchmark dataset, independent test dataset, model files, structural property information, attention mechanism details and web server usage) are available at Bioinformatics. online.

This paper proposes a new document retrieval (DR) and plagiarism detection (PD) system using multilayer self-organizing map (MLSOM). A document is modeled by a rich tree-structured representation, and a SOM-based system is used as a computationally effective solution. Instead of relying on keywords/lines, the proposed scheme compares a full document as a query for performing retrieval and PD. The tree-structured representation hierarchically includes document features as document, pages, and paragraphs. Thus, it can reflect underlying context that is difficult to acquire from the currently used word-frequency information. We show that the tree-structured data is effective for DR and PD. To handle tree-structured representation in an efficient way, we use an MLSOM algorithm, which was previously developed by the authors for the application of image retrieval. In this study, it serves as an effective clustering algorithm. Using the MLSOM, local matching techniques are developed for comparing text documents. Two novel MLSOM-based PD methods are proposed. Detailed simulations are conducted and the experimental results corroborate that the proposed approach is computationally efficient and accurate for DR and PD.

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