Next generation sequencing

Question 1

Explain the steps in NGS

Answer 1

flow cell channels

PCR

bridge amplication

Question 2

What are the 2 types of end sequences? Explain.

Answer 2

Single end sequence
reads from one end of a fragment - reps, polymorphs, missing data - limit

paired end sequence
-more efficient - help link contigs into scaffolds

Question 3

What type of software read the raw DNA data? What’s its format?

Answer 3

base-calling(phred)

FASTQ

Question 4

What is genome assembly? 2 strategies used?

Answer 4

ss

Question 5

explain de-novo sequence assembly? graphs created?

Answer 5

de brujin

Question 6

reads, contigs, scaffolds?

Answer 6

ss

Question 7

What features are in a genome annotation?

Answer 7

genes

repetitive

gc content & other nu compositions

Question 8

Explain the approaches to finding protein-coding genes in genomic dna?

Answer 8

extrinsic - homology-based & reference based

intrinsic-algorithmic
features analyzed?

Question 9

Gene prediction programs?

Answer 9

fgenesh, genscan

Question 10

what is GBrowse?

Answer 10

ss