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Data Analysis

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Year 2 Quiz on Data Analysis, created by gina_evans0312 on 28/12/2013.
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Quiz by gina_evans0312, updated more than 1 year ago
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Created by gina_evans0312 almost 11 years ago
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Resource summary

Question 1

Question
What is done in pairwise alignment?
Answer
  • Two sequences are stuck on top of each others and the common areas lined up
  • Two sequences are aligned from the beginning and their similarity analysed
  • Two sequences are aligned and their similarity analysed

Question 2

Question
Local alignment assigns correspondences to all residues in the sequence, leaving gaps if necessary
Answer
  • True
  • False

Question 3

Question
The image shows which of the following?
Image:
Indel (image/png)
Answer
  • An indel
  • A mismatch

Question 4

Question
The image shows a mismatch
Image:
Mismatch (image/png)
Answer
  • True
  • False

Question 5

Question
What can sequence identity be used for?
Answer
  • DNA sequence
  • Amino acid sequence
  • Gene sequence

Question 6

Question
Sequence identity can be how specific?
Answer
  • Global
  • Local

Question 7

Question
What are GAPS?
Answer
  • Spaces in part of the sequence that allows other areas to align better
  • Areas with a high density of indels
  • Proteins that align when sequences are swapped over

Question 8

Question
What is the scoring system that determines an optimal alignment?
Answer
  • +2 Match -1 Indel -2 Mismatch
  • +2 Mismatch -1 Match -2 Indel
  • +2 Match -1 Mismatch -2 Indel

Question 9

Question
Needleman and Wunsch algorithms find the highest scoring path across a matrix
Answer
  • True
  • False

Question 10

Question
Which is the light grey, and which is the dark grey?
Image:
Homologues (image/png)
Answer
  • Light- Remote homologues Dark - Close homologues
  • Light- Close homologues Dark- Remote homologues

Question 11

Question
PAM matrices used varies depending on the S.I
Answer
  • True
  • False

Question 12

Question
PAM250 scoring is used for remote homologues
Answer
  • True
  • False

Question 13

Question
In PAM250 scoring, scores are given based on what?
Answer
  • The residue rarity
  • The properties of the replacing residue- i.e. is one small hydrophobic residue replacing another

Question 14

Question
What does BLAST stand for?
Answer
  • Basic Loci Alignment Search Tools
  • Basic Loci Alignment Sequencing Tools
  • Basic Local Alignment Search Tools

Question 15

Question
What is different about BLAST techniques?
Answer
  • The compare residue 'words' instead of single residues/bases
  • They work in areas of less than 50bp long
  • They cover the whole genome very rapdily

Question 16

Question
A 'word' is 3bp or 11 aa long
Answer
  • True
  • False

Question 17

Question
Once the words have been found in the sequence, they are compared to the database- why?
Answer
  • To find exact matches
  • To find evolutionary relationships
  • To detect how common the words are

Question 18

Question
An E value is expectation, not probability
Answer
  • True
  • False

Question 19

Question
What is the range and significance for the E value? Smaller values are more likely
Answer
  • 0-10
  • 1-2
  • 0-1
  • 0.5
  • 5
  • 0.005

Question 20

Question
The E value is the probability of getting a result by change in a database of this size
Answer
  • True
  • False

Question 21

Question
What is the difference between P and E values
Answer
  • Both are values for 'What is the probability of getting this result by chance alone?', but P accounts for database size
  • Both are values for 'What is the probability of getting this result by chance alone?', E accounts for database size

Question 22

Question
In P values, <0.05 is significant
Answer
  • True
  • False

Question 23

Question
P value relies on a normal distribution
Answer
  • True
  • False

Question 24

Question
What are the limits of P?
Answer
  • 0-0.1
  • 0-1
  • 0-10

Question 25

Question
An E of 4 is equal to - in a database of this size, I could get 4 matches by chance alone
Answer
  • True
  • False
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