Module 5

Question 1

Sanger sequencing

Answer 1

1. Primer with 3’ end base pairs to a single stranded DNA template
2. Generate nested DNA fragments that vary by only 1 nucleotide
3. Nested fragments are sorted by size
4. Fragments start with a common 5’ sequence

Question 2

ddNTP

Answer 2

A dNTP that is missing the 3’ OH group and cannot form phosphodiester bonds

Question 3

PAGE

Answer 3

PolyAcrylamide Gel Electrophoresis allows for high resolution separate by fragment size

Question 4

Automated sanger sequencing

Answer 4

Fluorescent dyes are attached to ddNTPs to replace radioactive labels

Question 5

Parallelism

Answer 5

Many different reactions run at once

Question 6

Throughput

Answer 6

Amount of sequence information generated in a specific time

Question 7

Next generation sequencing technologies steps

Answer 7

1. template preparation
2. sequencing chemistry and detection
3. data analysis

Question 8

Illumina

Answer 8

Sequencing by synthesis, massively parallel, uses reversible fluorescently labeled ddNTPs

Question 9

Clonal bridge amplification

Answer 9

An oligo complimentary binds to an adapter region and forms a bridge where polymerase turns it into a double stranded bridge, creating two oligo strands

Question 10

Paired ends

Answer 10

An application that sequences the ends of a DNA fragment

Question 11

SMRT

Answer 11

Single molecule real time sequencing harnesses the natural power of DNA polymerase activity and detects DNA synthesis in real time

Question 12

Nanopore

Answer 12

A protein with a hole in the middle that is set in an electrically resistant membrane

Question 13

Bioinformatics

Answer 13

The intersection of biology, computer science, and informational tools

Question 14

Chromatogram/Electropherogram

Answer 14

Output sequence reads

Question 15

Phred

Answer 15

Base-calling algorithm used to interpret and check quality of sequence reads. Calculates the likelihood that a base call is incorrect

Question 16

Q score

Answer 16

The higher the score, the higher the quality of sequence and smaller likelihood of base-calling error

Question 17

Contig

Answer 17

One contiguous stretch of two or more reads

Question 18

Phrap

Answer 18

Algorithm that assembles 2 or more sequences that contain overlaps

Question 19

Pairwise alignments

Answer 19

Identifies regions of similarity

Question 20

Coverage

Answer 20

The average number of reads that cover a particular position in a sequence

Question 21

Consensus

Answer 21

Resulting final contiguous sequence of the aligned reads

Question 22

FastA format

Answer 22

Consensus contig sequence format

Question 23

GenBank

Answer 23

DNA sequence bank

Question 24

Entrez

Answer 24

Search engine that integrates different resources of NCBI

Question 25

BLAST

Answer 25

Used for unidentified sequence of nucleotides

Question 26

E value

Answer 26

The lower the E value, the greater the similarity

Question 27

OrfFind

Answer 27

Enter sequence data in FastA format to locate and identify genes within a sequence