Basic Applied Bioinformatics

CHAPTER 34Prediction of Translation Initiation Sites

S Jain¹, S Panwar² and A Kumar³

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

34.1 INTRODUCTION

The correct recognition of translation initiation sites (TIS) can help us to understand the gene structure and its product. The computational identification of TIS is the main constituent of the gene prediction system and, therefore, has utmost importance in genome annotation. Lots of data mining methods have been employed to identify TIS in transcripts such as mRNA, EST and cDNA sequences. All these methods are based on the scanning model (Kozak, 1989), which states that, in eukaryotes, the first “AUG” (start codon) at the 5′ prime of the mRNA transcript is usually the exact TIS. However, exceptions can occur via the process of leaky scanning, re‐initiation and internal initiation of translation, which results in another AUG being the true TIS.

The consensus motif GCCRCCatgG around the TIS was probably the first effort to identify TIS with statistical meaning (Salamov et al., 1998). The general approach for answering the TIS prediction difficulty is to create the numerical data from the cDNA sequences and, subsequently, apply computational methods.

34.2 OBJECTIVE ...