Bioinformatics

Question 1

What is systems biology?

Answer 1

The study of the interactions between components of biological systems and the function and behaviour they provide.

Question 2

What is the cycle of biological science discovery?

Answer 2

New hypothesis
Experiment 
New data
Model construction
Model analysis
Biological insight

Question 3

What is sequence identity?

Answer 3

A perfectly matched sequence

Question 4

What is sequence homology?

Answer 4

A partially matched sequence

Question 5

What are gene predictions built around?

Answer 5

Pattern recognition

Question 6

What search does DNA fingerprinting use?

Answer 6

Homology search using microsatellites- small arrays of tandem repeats

Question 7

What is the evolutionary theory based on?

Answer 7

The similarities in biological sequences

Question 8

What is sequence annotation?

Answer 8

The process of identifying similarities between different biological sequences

Question 9

How does sequence homology work?

Answer 9

It compares an unknown sequence against a database of known sequences

Question 10

Which databases contain DNA sequences?

Answer 10

ENA/EMBL
GenBank
DDBJ

Question 11

Which databases contain protein sequences?

Answer 11

UniProtKB

RefSeqP

Question 12

What is the algorithm used to compare an unknown sequence to known sequences?

Answer 12

A pairwise sequence alignment

Question 13

What are the two types of alignment and what do they mean?

Answer 13

Global- aligns the whole sequence

Local- aligns domains and subsequences so some parts are unrelated

Question 14

How are alignments produced?

Answer 14

A score is produced for each match or mismatch. If the score reaches a threshold it is reported.

Question 15

What are expressed sequence tags (ESTs)?

Answer 15

cDNA produced from mRNA so only contain exons not introns.

Only a local alignment could be used with these sequences

Question 16

What is the standard format that programs require?

Answer 16

Fasta format

Question 17

What is Fasta format?

Answer 17

> description of the sequence

The sequence on the subsequent lines

Question 18

What is BLAST?

Answer 18

Basic local alignment search tool

Question 19

What is blastn?

Answer 19

Search for a nucleotide using a nucleotide query

Question 20

What is blastp?

Answer 20

Search for a protein using a protein query

Question 21

What is blastx?

Answer 21

Search for a protein using a translated nucleotide query

Question 22

What is tblastn?

Answer 22

Search for a translated nucleotide using a protein query

Question 23

What is tblastx?

Answer 23

Search for a translated nucleotide using a translated nucleotide query

Question 24

What are the 5 BLAST outputs?

Answer 24

Score
Identities
Positives
Gaps
E-Value

Question 25

What does the score show in a BLAST output?

Answer 25

The matches - mismatches

Question 26

What does the identity show in a BLAST output?

Answer 26

The number of identical residues

Question 27

What does the positives show in a BLAST output?

Answer 27

The number of similar residues

Question 28

What does the gaps show in a BLAST output?

Answer 28

The number of gaps introduced to give the best alignment

Question 29

What does the E-Value show in a BLAST output?

Answer 29

The reliability of the alignment calculated by expected alignments and chance of alignments.

Question 30

What is a good E-Value in a BLAST output?

Answer 30

A value less then 1e^-3

Question 31

Define similar residues

Answer 31

Residues that have yet he same chemical and physical properties

Question 32

Name 6 different properties of amino acids

Answer 32

``` Hydrophobic Aliphatic Aromatic Small Charged Polar ```

Question 33

What is a protein domain?

Answer 33

A part of the protein structure that evolves function and can exist independently. They are between 25 and 500 residues long and appear in evolutionary related proteins

Question 34

What are some example protein domain functions?

Answer 34

``` Ligand binding Spanning the plasma membrane Containing the catalytic site DNA- binding Surface to bind to other proteins ```

Question 35

Give an example of a domain database

Answer 35

CDD | InterPro

Question 36

What is a multiple sequence alignment?

Answer 36

It aligns several sequences

Question 37

What is a multiple sequence alignment tool?

Answer 37

Clustal

Question 38

What 2 algorithms are used in a multiple sequence alignment?

Answer 38

Position specific scoring matrices (PSSM) | Hidden Markov Model (HMM)

Question 39

What is found in a Clustal output?

Answer 39

* entirely conserved column : roughly the same size and hydrophobicity . Conserved size or hydrophobicity

Question 40

What does an output from Clustal of a good multiple sequence alignment contain?

Answer 40

10-30 residues 1-3 stars (*) 5-7 colons (:) A few full stops (.)

Question 41

Why are multiple sequence alignments useful?

Answer 41

To show sequence conservation, particularly domains Identify a particular conserved residue Determine secondary and tertiary structures To build phylogenetic trees to show evolutionary origins

Question 42

What are phylogenetic trees used for?

Answer 42

To construct an evolutionary relationship between species or sequences

Question 43

What is a rooted phylogenetic tree?

Answer 43

Each node represents the most recent common ancestor. The line corresponds to time

Question 44

What is an unroofed phylogenetic tree?

Answer 44

This makes assumptions about relatedness without ancestry. If an ancestor is identified the tree can be converted to a rooted tree

Question 45

How are phylogenetic trees rooted?

Answer 45

Using an outgroup that is closely related to the groups but less closely related than the other groups are to each other. The trees require related sequences or multiple sequence alignments

Question 46

What 6 things can you find using bioinformatics?

Answer 46

``` Gene prediction Sequence analysis Protein structure prediction Epidemiology Microarray data analysis Metabolic pathway modelling ```