Week 1Bioinformatics, genomics, and our model organism
What the field is, how genome sequencing got from a 3,569-base phage to a 17-gigabase wheat, and the bacterium we will use for everything that follows.
Questions this week answers
What does bioinformatics do that biology on its own cannot?
Genome sizes went from 3,569 bases to 17 gigabases in forty years. If size stopped being the barrier, what replaced it?
Why can two strains of the same species share fewer than half their genes?
By the end of this week you can
Say what bioinformatics is and how it differs from computational biology
Place the landmark genomes on a timeline and explain why the sizes jump
Explain why two strains of one species can share fewer than half their genes
Name the gene families that make a rhizobium able to fix nitrogen
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Two definitions worth keeping apart
Bioinformatics develops methods and software for understanding biological data, especially when the data are large and complex.
Computational biology is the subsequent process of analysing and interpreting that data.
Computational genomics is computational and statistical analysis used to decipher biology from genome sequences.
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What should survive this week
Bioinformatics builds the methods; computational biology applies them. The distinction is the same one as between this course's lectures and its tutorials.
Sequencing stopped being the hard part. Complexity, ploidy and repeats did not, which is why a 17 Gb hexaploid wheat is harder than a 3 Gb human.
A species is not one genome. Only 39.2% of the combined E. coli proteins were present in all three strains compared.
nod, nif and fix are the thread. You will annotate them in week 5, compare them in week 7 and measure their expression in week 10.