Gene finding

Question 1

Define open reading frame (ORF)

Answer 1

A stretch of DNA whose length is a multiple of 3, that begins with the start codon (ATG) and ends with one of the 3 stop codons (TAA, TAG, TGA)

Question 2

Define frameshift mutation

Answer 2

Mutation that inserts or deletes a nucleotide/nucleotides

Question 3

Explain evidence-based gene finding

Answer 3

Identify RNA or protein sequences and map them back to the genome

Question 4

Explain ab initio gene prediction

Answer 4

1. Find open reading frames (ORFs)
2. Test the probability of ORFs appearing by chance via statistical approaches or matching against a database of known motifs

Question 5

Explain gene finding by comparative genomics approach

Answer 5

detect conserved DNA regions by comparing a large set of related genomes

Question 6

Define homolog

Answer 6

A gene related to a second gene by descent from a common ancestral DNA sequence.

Question 7

Define ortholog

Answer 7

Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution.

Question 8

Define paralog

Answer 8

Paralogs are genes related by duplication within a genome. Paralogs can have differrent functions.

Question 9

Explain randomization test

Answer 9

Simulate random data according to null model.

The p-value is the fraction of simulated data that have a higher value for the test statistic than the observed one.