4. Bioinformatics

Question 1

bioinformatics

Answer 1

the development and application of computer science to the analysis of large amounts of biological information

Question 2

key elements of bioinformatics

Answer 2

• algorithms and statistical analysis
• software tool implementation
• database infrastructure to store and access data

Question 3

typical bioinformatics workflow

Answer 3

sequence DNA
-> Assemble sequence
-> identify genes
-> assign genes to groups/clusters
-> find gene functions and protein sequences
-> identify variation and 3D structure

Question 4

Protein domain identification

Answer 4

using InterProScan
- compares protein to known domain functions
eg. LacI protein has a DNA-binding domain and a regulatory domain

Question 5

3D structure prediction

Answer 5

Alpha fold
input sequence-> database search-> multiple sequence alignment-> covariation -> prediction

Question 6

protein variation effect prediction

Answer 6

ClinVar: database of known variants and clinical significance
AlphaMissense: predicts clinical significance of variants

Question 7

Blast- query

Answer 7

Searched sequence

Question 8

BLAST subject

Answer 8

compared gene sequence

Question 9

BLAST CDS

Answer 9

amino acid coding sequence

Question 10

BLAST CDS number

Answer 10

location in amino acid sequence

Question 11

BLAST Score

Answer 11

number of gene matches found, not including mismatches

Question 12

BLAST Expect

Answer 12

chance of this match occurring coincidentally in this database

Question 13

BLAST identity

Answer 13

similarity between Sbjct and Query and how many changes have occurred between them

Question 14

Gaps

Answer 14

missing regions of sequence, indicates InDel mutations

Question 15

BLAST strand

Answer 15

shows which direction the strands are oriented
+ = 5’ - 3’
- = 3’ - 5’