NGS

• Gene Finding
• Transcription Process

  first step in gene expression, It involves copying a gene's DNA sequence to make an RNA molecule. This process is carried out by RNA polymerase.

  
• Ribosomes


  Manufacture proteins based on mRNA instructions

  
• Translation


  How Ribosome Synthesizes Proteins

  
• Genetic Code


  • TAA
  • TGA
  • TAG
  • ATG
• Gene Structure of Prokaryotic Cells
• Gene Info


  • A DNA sequence coding for the pre-mRNA
  • An additional DNA code or other regulating process, which regulates the alternative splicing

  
• Alternative Splicing
• Classes of Gene predictors

  • Ab initio
  • De novo
  • EST/cDNA-based & combined approaches

  
• Signals for Gene Finding

  the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome.
• Exon and Intron Lengths
• Nucleotide Composition
• HMMs for Gene Recognition

  
• Using Comparative Information
• Patterns of Conservation
• Gene-Finding Algorithm


  1. Scan each of 3 ORFs, and find subsequence that start with ATG and end with one of (TAA, TAG, TGA)

  2. Repeat above for the complementary sequences also

  
• Risk of the Simple Gene Finding Algorithm
• Calculating p
• Comparison-based Gene Finders


  • Rosetta, 2000
  • CEM, 2000
  • Twinscan, 2001
  • SLAM, 2002
  • NSCAN, 2006

  
• Motifs

  recurring patterns or sequences of nucleotides (DNA or RNA) or amino acids (in proteins) that serve specific functions.
• Intergenic regions

  • Intergenic regions are non-coding segments of DNA that do not contain any protein-coding genes.
  • They separate one gene from another within the genome.
• Intergenic regions function:

  • Although they do not directly encode proteins, intergenic regions play essential roles:
  • Gene Regulation: Regulatory elements within intergenic regions control gene expression by interacting with transcription factors.
  • Spacer Regions: Intergenic regions provide physical spacing between genes, preventing interference during transcription and translation.
  • Evolutionary Significance: Changes in intergenic regions can impact gene regulation and contribute to species diversity.
• Open Reading Frame (ORF)

   is a portion of a DNA sequence that does not include a stop codon.
• Reading Frames:

  • DNA has two strands, and ribosomes can read RNA derived from either strand.
  • This leads to six different reading frames for every piece of DNA, potentially yielding multiple ORFs.