Lecture 6

Question 1

What forms of repetitive sequences are dominant contributors to genome size variation?

Answer 1

• Highly repetitive
• Moderately repetitive

Question 2

What are 2 approaches to genome sequencing?

Answer 2

• Top down
• Bottom up

Question 3

What is the “top down” approach to genome sequencing?

Answer 3

• Break large sequences into smaller pieces which overlap
• These pieces cover the whole genome
• Fragment these pieces, sequence

Called Hierarchical (or clone contig) sequencing (HS)

Question 4

What is the “bottom up” approach to genome sequencing?

Answer 4

• Fragment wholegenome into small pieces
• Sequence and assemble

Called Whole Genome Shotgun (WGS)

Question 5

What is a main obsticle of shotgun sequencing?

Answer 5

Repetitive genomes (with tandem and interspersed repeats) are difficult to assemble correctly

Question 6

How do you overscome the problem of small high copy number repeats (Like Alu elements) and large segmental duplications in WGS?

Answer 6

Sequence ends of larger clones (10kb-15kb) to confirm maintainance of genome wide repeat arrays in assembled sequence

Question 7

List 3 pros and cons for HS

Answer 7

Pros:

• Accurate
• Coverage Known
• Sequential

Cons:

• Slow
• Expensive
• Map dependent

Question 8

List 3 pros and cons for WGS

Answer 8

Pros:

• Fast
• Cheap
• Map independant

Cons:

• Accuracy
• Coverage is estimated
• Periodic

Question 9

List 2 types of sensors for geen identification

Answer 9

• Signal sensors; detect short (disctrete) sequence motifs (consensus); eg start/stop codons, splice donor/acceptor sites
• Content sensors; detect long (extended) sequence motifs (no consensus); eg CpG islands (vertebrates), coding vs intergenic

Question 10

What are long open reading frames (ORFs) indicative of?

Answer 10

Genes

Question 11

What is high gene density indicative of in ORFs?

Answer 11

• Long ORFs
• Little intergenic DNA

Question 12

What is low gene density indicative of in ORFs?

Answer 12

• Short ORFs (Exons)
• Much intergenic DNA

Question 13

List 2 problems with ORF detection

Answer 13

• Short exons are ignored (by chance)
• Boundaries missed (start codons, untranslated exons)

Question 14

What is the ab initio method of gene prediction?

Answer 14

• Infering candidate gene existance
• Done by identifying appropriate arrangements of sensor features and content features

Question 15

What is the ab initio and homology method of gene prediction?

Answer 15

• Test candidate gene similarity to know genes (BLASTP)

Question 16

How do Hidden Markov model programs function?

Answer 16

Build explicit methmatical models using training data

Question 17

What is sensitivity in regards to gene predictions?

Answer 17

Ratio of true positives (predicted) to actual (confirmed) positives

Question 18

What is specificity in regards to gene predictions?

Answer 18

Ratio of true positives to predicted positives