Gene prediction and annotation

Question 1

Identification of genes

Answer 1

• Prokaryote
  
  • generally easy
  • sequence without interruptions
• Eukaryotes
  
  • more difficult (exons are divided)

Question 2

What is gene prediction?

Answer 2

• the identification of genetic elements in a genomic sequence

Question 3

How is gene prediction done?

Answer 3

• de-novo predictions
  
  • training set
• evidence Based
  
  • EST, Proteins, RNAseq
• comparatve genomics
  
  • other genomes
  • useful in the discovery of functionally relevant regions
• combiner
  
  • training set

Question 4

GBROWSE

Answer 4

• tool for the visualization of genetic annotations
  
  • based on a relational database
• helps in the understanding of the predictions
  
  • de novo prediction using different predictors: many false positives
  • alignment of EST and proteins: very good but not all genes are covered
  • objects in the Gbrowser can be linked to the annotation platform

Question 5

Genetic annotations

Answer 5

• process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do
• is a note added as a commentary

Question 6

Functional annotation

Answer 6

• process of attaching biological information to sequences of genes or proteins
• two methods
  
  • Automatic annotation
    
    • relatively fast
    • generally inferred from sequence similarity
    • useful as starting point
  • Manual annotation
    
    • requires experts
    • long process

Question 7

Gene ontology

Answer 7

• controlled, structured and dynamic dictionary of biological processes, molecular functions and cellular components
  
  • can be applied to all organisms
• tool for the unification of biology
• easier comparison among different species
• annotations have evidence codes
  
  • information about the evidence from which the annotation has been made.

Question 8

Gene ontology typer of annotations?

Answer 8

• electronic annotation
  
  • relatively quick
  • large number of annotations
  • sequence similarity and mapping
  • useful for not well known genomes
• manual annotation
  
  • high-quality annotation
  • expert biologists needed
  • time consuming

Question 9

Markov chains

Answer 9

• predicting events
  
  • stochastic model describing a sequence of possible events in which the probability of each event depends only on the state attained in the previous event
• can predict whether a certain text belongs to one language or another
  
  • can be used to detect signatures in DNA and amino acid sequences
  • discriminate between coding and non-coding regions (de novo)
• Hidden Markov Models (HMM) states are not directly visible