Unit 11: Genomics, Bioinformatics, and Comparative Genomics
Reading and comparing whole genomes at once, and what that scale reveals that gene-by-gene genetics never could.
6 topics · 21 questions
Each topic is a path, not a menu: work down it in order and every question builds on the one above. Click any of them to watch the answer draw itself.
Whole-Genome Sequencing and Assembly
- How it worksHow do overlapping sequence reads get computationally reassembled into one continuous genome?
- Going furtherWhat happens to genome assembly accuracy when a genome contains long stretches of repetitive sequence?
- Common mistakeWhy doesn't sequencing a genome once guarantee that every base has been read correctly?
- Worked exampleFind the minimum sequencing depth needed so a genome position is covered by at least 10 overlapping reads on average.
Your turn1 of 2
A genome of 1544626 bases is sequenced using 35960 reads, each 286 bases long. What is the average sequencing depth (coverage) at each genome position?Bioinformatics and Sequence Alignment
- How it worksHow does a sequence alignment algorithm score matches, mismatches, and gaps to find the best alignment?
- Worked exampleFind the percent identity between two 20-base sequences that align with 17 matching positions.
- Ties togetherHow does sequence alignment let researchers use one organism's known gene to identify its counterpart in another species?
Your turn1 of 2
Two sequences, each 48 bases long, are aligned, and all but 6 positions match exactly. What is the percent identity between the two sequences?Comparative Genomics and Synteny
- How it worksHow does conserved gene order, called synteny, reveal which chromosome regions descended from a shared ancestor?
- Going furtherWhat happens to synteny between two species' genomes the further back their common ancestor lived?
- Common mistakeWhy doesn't having the same number of genes mean two species are closely related?
- Worked exampleFind how many of ten genes remain in the identical order when comparing a syntenic block across two related species.
Your turn1 of 2
Two unrelated species happen to have almost the exact same total number of genes. Does this mean the two species are closely related?Gene Density and Noncoding DNA
- How it worksHow do introns, regulatory regions, and repetitive elements make up the noncoding majority of a genome?
- Going furtherWhat happens to genome size across species that does not track cleanly with an organism's apparent complexity?
- Common mistakeWhy isn't noncoding DNA automatically useless junk with no function at all?
Your turn1 of 2
Less than 2 percent of the human genome actually codes for protein, so a huge majority is noncoding. Why isn't this noncoding DNA automatically dismissed as useless junk with no function at all?The Human Genome Project
- How it worksHow did the Human Genome Project combine many labs' overlapping sequence data into one reference genome?
- Ties togetherHow did the Human Genome Project's reference sequence make modern genomics and personalized medicine possible?
- Going furtherWhat happens to medical research once a disease gene can be located against a complete reference genome instead of searched for blind?
Your turn1 of 2
The Human Genome Project's reference sequence became a foundational resource for essentially all of modern genomics and personalized medicine. How specifically did having one complete reference sequence make this possible?RNA-Seq and Genome-Wide Gene Expression
- How it worksHow does RNA-seq count sequencing reads per gene to measure how strongly each gene is expressed?
- Worked exampleFind which of two genes is more highly expressed given gene A gets 800 reads and gene B gets 200 reads from the same RNA-seq run.
- Common mistakeWhy doesn't a gene's DNA sequence alone tell you how much of its protein a cell is actually making?
- Going furtherWhat happens to a genome-wide expression profile when the same tissue is compared between a healthy sample and a diseased one?
Your turn1 of 2
In an RNA-seq run, gene A gets 1423 sequencing reads and gene B gets 667 sequencing reads. Approximately how many times more highly expressed is gene A than gene B?