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J Theor Biol. 2011 Oct 21;287:92-9. doi: 10.1016/j.jtbi.2011.07.017. Epub 2011 Aug 3.

BacPP: bacterial promoter prediction--a tool for accurate sigma-factor specific assignment in enterobacteria.

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1
Universidade de Caxias do Sul, Programa de Pós-Graduação em Biotecnologia, Av. Francisco Getúlio Vargas, 1130-CEP 95070-560, Caxias do Sul-RS, Brazil. sasilva6@ucs.br

Abstract

Promoter sequences are well known to play a central role in gene expression. Their recognition and assignment in silico has not consolidated into a general bioinformatics method yet. Most previously available algorithms employ and are limited to σ70-dependent promoter sequences. This paper presents a new tool named BacPP, designed to recognize and predict Escherichia coli promoter sequences from background with specific accuracy for each σ factor (respectively, σ24, 86.9%; σ28, 92.8%; σ32, 91.5%; σ38, 89.3%, σ54, 97.0%; and σ70, 83.6%). BacPP is hence outstanding in recognition and assignment of sequences according to σ factor and provide circumstantial information about upstream gene sequences. This bioinformatic tool was developed by weighing rules extracted from neural networks trained with promoter sequences known to respond to a specific σ factor. Furthermore, when challenged with promoter sequences belonging to other enterobacteria BacPP maintained 76% accuracy overall.

PMID:
21827769
DOI:
10.1016/j.jtbi.2011.07.017
[Indexed for MEDLINE]

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