Struggle

Question 1

What is bioinformatics?

Answer 1

It is the analysis and conceptualisation of complex biological information.

Question 2

What us BLOSUM62

Answer 2

is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. They are based on local alignments. Pairwise alignment greater than 62%

Question 3

Explain Affine Gap Penalties

Answer 3

Penalises insertions/ deletions, Penalty for gap openings, gap extensions, length of gap extensions. Gap openings have a higher cost.

Question 4

What is In Silico

Answer 4

Ligand analysis performed on a computer

Question 5

Explain BLAST

Answer 5

(basic local alignment search tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. It uses Heuristic to speed us computation

Question 6

What is Dynamic Programming

Answer 6

dynamic programming is solving complex problems by breaking them into states. It gives a score to find the optimal alignment. This process is very slow. The steps involve 1. initialisation 2. scoring the matrix 3. traceback

Question 7

Protein vs DNA

Answer 7

Protein has 20 characters rather than 4. Codons are degeneratable. Offers a longer look back in time.

Question 8

Paralogs

Answer 8

Duplication event

Question 9

Why is DNA used?

Answer 9

To identify cDNA, non-coding regions of DNA and to identify DNA polymorphorisms.

Question 10

Types of Algorithms?

Answer 10

1. Uniformative
2. Ungapped
3. Gapped

Question 11

Describe a hierarchical approach?

Answer 11

1. Different groups are given a chromsome to sequence
2. The hroups genereate a bacterial artifical chromosome (BAC)
3. BAC is divided and shothun sequences
4. High fideltiy maps identify motifs and allow detection of overlapping sequences.

Question 12

How many Genes were found

Answer 12

51k

Question 13

How many genes code

Answer 13

20k

Question 14

How many genes non code

Answer 14

20k

Question 15

What are pseudo genes

Answer 15

genes that seem to be protein coding but mutation renderers them non coding. 18k found

Question 16

How many mRNA’s found? and what does this mean?

Answer 16

98k, for every gene, 5 mRNA are made.

Question 17

Why are MSA done?

Answer 17

To elucidate functional in formation with proteins. Perform evolutionary analysis.

Question 18

How are alignments scored?

Answer 18

1. Maximum number of sequences are matched.
2. Scoring is done with Sum of Pairs
3. Each column is scored by summing all possible matches, gaps and mismatches.

Question 19

What is the E-value?

Answer 19

The Expect value (E) is a parameter that describes the number of hits one can “expect” to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases.

Question 20

What us the Affine Gap penality

Answer 20

Large opening gap penalty. smaller penalty for extending gap.

Question 21

Neighbour Joining

Answer 21

Similar to UPGMA, corrects evolutionary rate. Created unrooted tree

Question 22

What are some ways to create a tree?

Answer 22

1. Distance Matrix Method
2. Maximum parsimony method
3. Maximum likelihood method

Question 23

What is bootstrapping?

Answer 23

A way of statistically validating a tree

Data is resampled

Question 24

How is MSA measured

Answer 24

It uses the ClustalW to form a phylogenetic tree. It uses the Sum of Pairs (Heuristic)

Question 25

How does CLUSTAL work?

Answer 25

1. Begin with a pairwise alignment 2. Build a phylogenetic tree 3. Take the most closely related sequence and align them 4. Repeat with the next most closely related sequence

Question 26

What is a characteristic of a fully resolved tree?

Answer 26

Only two branches on each node

Question 27

Describe the distance matrix method?

Answer 27

Distance-based methods must transform the sequence data into a pairwise similarity matrix for use during tree inference. 10. UPGMA. Stands for Unweighted pair group method with arithmetic mean.

Question 28

Character based method

Answer 28

Use the aligned sequences directly during | tree inference.

Question 29

Describe the shotgun approach

Answer 29

1. DNA is isolated and chopped into fragments 2. Fragments are cloned into vectors and sequenced 3. Overlapping genes contribute to assemble the genome into contigs 4. Scaffolds resemble contigs

Question 30

Output of Sanger Sequencing

Answer 30

500-1k

Question 31

Output of NGS

Answer 31

Billions

Question 32

Sanger sequencing?

Answer 32

The target DNA is copied many times, making fragments of different lengths. Fluorescent “chain terminator” nucleotides mark the ends of the fragments and allow the sequence to be determined.

Question 33

What determines the conformations of a protein active site

Answer 33

The conformations of side chains of the proteins non-active site regions

Question 34

Describe the difference between local and global alignment.

Answer 34

global and local. The global approach compares one whole sequence with other entire sequences. The local method uses a subset of a sequence and attempts to align it to subset of other sequences. Local alignments reveal regions that are highly similar, but do not necessarily provide a comparison across the entire two sequences.

Question 35

Explain the steps of BLAST

Answer 35

1. break the query into short words of a specific length. 2. These words are then compared against a sequence in a database. 3. those words whose T value was greater than 18 were used as seeds to extend the alignment.

Question 36

What does an E value of 1 represent

Answer 36

An e value of 1 means that one alignment using a query of this size will by chance produce a S score of this value in a database of this size.