Title: Transcription Factor mapping between Bacteria Genomes

Authors: Rachita Sharma, Patricia A. Evans, Virendrakumar C. Bhavsar

Addresses: Faculty of Computer Science, University of New Brunswick, P.O. Box 4400, 540 Windsor Street, Gillin Hall, E126 Fredericton, NB E3B 5A3, Canada. ' Faculty of Computer Science, University of New Brunswick, P.O. Box 4400, 540 Windsor Street, Gillin Hall, E126 Fredericton, NB E3B 5A3, Canada. ' Faculty of Computer Science, University of New Brunswick, P.O. Box 4400, 540 Windsor Street, Gillin Hall, E126 Fredericton, NB E3B 5A3, Canada

Abstract: Identification of regulatory elements, such as Transcription Factors (TFs), is useful in construction of regulatory networks and to understand gene regulation. These TFs have already been recognised for model organisms based on extensive experiments but have not been as heavily investigated for non-model organisms. This paper proposes to use two versions of Basic Local Alignment Search Tool (BLAST), BLASTP and PSI-BLAST, to map the TFs from a model to a non-model organism. Experiments are performed on bacterial organisms based on evolutionary distance to compare the results. Analysis of the results suggests that TFs can be mapped from one bacterial organism to another, as TF motifs are well preserved among these organisms. Results are also analysed to determine the best suitable threshold for the e-value parameter of BLAST that can be used to map TFs and the appropriate version of BLAST to use. Both the BLAST e-value threshold and evolutionary distance from the model organism used for mapping have significant impact on the quality of results.

Keywords: TFs mapping; transcription factors; bacteria genomes; BLAST; basic local alignment search tool; BLASTP; PSI-BLAST; e-value; evolutionary distance; model organism; non-model organisms; Escherichia coli; Bacillus subtilis; regulatory networks; gene regulation; TF motifs.

DOI: 10.1504/IJFIPM.2009.030837

International Journal of Functional Informatics and Personalised Medicine, 2009 Vol.2 No.4, pp.424 - 441

Published online: 08 Jan 2010 *

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