Wk2: Microbial Bioinformatics

Question 1

What has bioinformatics contributed to?

Answer 1

• Predicting and visualising protein structure using data and algorithms - proteins
• Assembling sequence fragments to obtain the whole genome sequence - nucleotide sequences
• Analysing data from transcriptome (gene and protein expressions and regulation)

Question 2

What examples of data can you retrieve from bioinformatics?

Answer 2

DNA sequencing of genes or full genomes, protein sequences

Question 3

What can information about genomes retrieved from bioinformatics provide?

Answer 3

It can allow researchers to compare different genomes of bacterial species

Question 4

How can we use genetic information to establish evolutionary relationships among species?

Answer 4

Retrieving genetic information such as SNP’s from bioinformatics across species allow researches to infer phylogeny (relationships among taxa) - measuring evolutionary distance

Question 5

What are statistical calculations that can be used for phylogenetic inference?

Answer 5

We can use the maximum likelihood to work out which set of trees amongst a few species is the truest one.
- Done by calculating and finding the likelihoods of each tree

Question 6

Can we use genetic sequences to establish evolutionary relationships among all cellular lifeforms?

Answer 6

No, as many genes are not shared by all bacteria

Question 7

Why is the 16S ribosomal RNA (genetic sequence) used to infer evolutionary relationships amongst cellular life?

Answer 7

Because in order to compare many different species, it is ideal to choose the gene sequence that is shared amongst all different species, hence using the 16S ribosomal RNA.

Question 8

How does the distance-based method work to infer phylogenetic trees and measuring evolutionary distance?

Answer 8

Look at the sequences to compare/record the number of differences between them, so you can construct a distant matrix and develop a phylogenetic tree.