March 20

Question 1

Define the following terms: Genome, Core genome, accessory genome, pangenome

Answer 1

Genome:The entirety of an organism’s hereditary information (can be DNA or RNA).

Core Genome: The genes that are present in all sequenced strains of a species.

Accessory Genome: All of the genetic elements that are not part of the core genome – including plasmids.

Pangenome: The set of genes encoded by the genomes of all strains of a species.

Question 2

How does Sanger sequencing work?

Answer 2

Include all dNTps, but only a small amount of a ddNTP, so at differerent spots for a given nucleotide the PCR stops for PCR. So know at these locations have these nuclotides

Question 3

How does shotgun sequencing work?

Answer 3

Randomly break DNA into fragments, so have overlapping parts, determine locations of these fragments

Question 4

Define draft genome, complete genome, read, contig, supercontig (scaffold)

Answer 4

Draft genome: A genomic DNA sequence of relatively low accuracy that has some missing segments (gaps) or contigs that in the wrong order or orientation.

Complete (or finished) Genome: A genomic DNA sequence of relatively high accuracy that has no ambiguity about the order or orientation of any segment and has few if any gaps.

Reads: They are fragments of DNA, and you have aligned common sequences with them to have parts of the puzzle. When use them to make 1 complete part of sequence, form a contig

Contig: Continous piece of DNA without gaps

Supercontig (scaffold): Composed of many contigs,