Gene Analysis Introduction

When a geneticist is given an unknown DNA sequence and is tasked with finding out its function, there are two approaches.  Ab initio, or “from the beginning” involves using programs that analyze the sequence for known trends in gene expression. These trends include translation initiation occuring at ATG, and intron boundaries being defined by GT at the beginning and AG at the end.  Stop codons include TAG, TAA, and TGA. Using these in combination with more complex trends of gene expression, ab initio programs can make a prediction about the coding sequence and protein sequence of a gene. The other method is homology based searches. These include comparing a query sequence to sequences of nucleic acids of a known origin. In this lab, we begin by building two predictions of the protein our gene encodes: one using ab initio methods and another using homology based methods.  For the ab initio method, we use the program FGENESH. For the homology based searches, we use Phytozome and NCBI BLAST. We compare the two predictions and proceed to research our gene of interest.  We then provide an assessment of function of our gene.