Transcription Factor mapping between Bacteria Genomes Online publication date:: Fri, 08-Jan-2010
by Rachita Sharma, Patricia A. Evans, Virendrakumar C. Bhavsar
International Journal of Functional Informatics and Personalised Medicine (IJFIPM), Vol. 2, No. 4, 2009
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.
Online publication date:: Fri, 08-Jan-2010
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