Gene Prediction

Question 1

What is computational gene prediction?

Answer 1

The process used to assemble a genome after sequencing.

Question 2

Three main automated gene prediction strategies.

Answer 2

Similarity based (BLAST)
Ab-initio - statistical models to make genomes from scratch
Combined evidence (combining gene models with alignment)

Question 3

Gene prediction in prokaryotes

Answer 3

Their genomes are typically small, 0.5 to 10mbp) with high gene density, contiguous stretches of ORFs.

Question 4

Shine-Delgarno sequence

Answer 4

Purine rich sequence upstream of start codon, complementary to 16S rRNA.

Question 5

ORF length test

Answer 5

Scanning for ORFS over 180 nucleotides in length to identify potential coding sequences.

Question 10

Codon usage significance in gene prediction

Answer 10

Codon usage analysis involves assessing the frequency of codons within an ORF.

Question 10

Markov models

Answer 10

Describes the probability distribution of nucleotides based on previous sequences.