Basic Applied Bioinformatics

CHAPTER 33Prediction of Transcription Binding Sites

S Jain¹, S Panwar² and A Kumar³

¹ Department of Applied Sciences & Humanities, Jai Parkash MukandLal Innovative Engineering and Technology Institute, Yamuna Nagar, Haryana, India

² Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Uttar Pradesh, India

³ Department of Nutrition Biology, Central University of Haryana, Haryana, India

33.1 INTRODUCTION

Transcription factors are crucial for sequence‐specific control of transcriptional regulation. Classically, the computational prediction of transcription factor binding sites (TFBS) depends on position weight matrices (PWMs) (Wingender et al., 2001), which give weights to each nucleotide at each position. These models strongly suggest that each nucleotide participates independently in the corresponding DNA–protein interaction and does not account for flexible length motifs.

33.2 OBJECTIVE

To predict the transcription binding site by using the TRANSFAC and MATCH tools

33.3 TRANSFAC

TRANSFAC is a database of TRANScription regulatory FACtors, and is maintained at GBF Braunschweig (Wingender et al., 2000). It combines the data regarding transcription factors, their DNA binding sites, sources of the factors and systematic classification of transcription factors. All the experimental results are accessible mainly through the FACTORS and the SITES table (Frech et al., 1997).

The data regarding binding proteins and the DNA sequences that are recognized by ...