Team I Gene Prediction Group

Members: Maria Ahmad, Hira Anis, Jessica Mulligan, Priya Narayanan, Aaron Pfennig, Winnie Zheng

Introduction

Prokaryotic Gene Feature

• Prokaryotic genes have a relatively well-understood promoter sequence, such as a regulatory sequence, which can regulate the transcription of the gene into an mRNA.
• Each prokaryotic gene has open reading frames(ORF) which start with start codons and end with end codons with no interruptions(end-codons) in-between, so it can provide a good, but not assured prediction of the protein-coding regions.

Gene Prediction

Gene prediction or gene finding is a process of identifying the regions of genomic DNA that encode genes. It is devised two-classes of methods that use similarity-based(homology) searches and ab initio prediction to capture the compositional differences among coding regions which will be translated into protein and noncoding DNA which can be translated into tRNAs and rRNAs.

Project Goal

The main goal of our project is to finish the gene prediction for the assembled gene from E.coli given by the previous group.

Methods

Ab-initio Methods(CDS prediction)

• Predicting protein-coding genes in a given genome based on certain features.
  • ORFs
  • Signal Sensor: Regulatory motifs(RBS, SD, etc)
  • Content Sensor: The codon usage bias, based on GC content, can help to distinguish coding sequence from surrounding non-coding sequence.