When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs. What is the difference between physical and sequence gaps?

When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs. Why were there so many more contigs than scaffolds?

When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs.

How can sequence gaps be closed?

How do cDNA sequences facilitate gene annotation? Describe how the use of full-length cDNAs facilitates discovery of alternative splicing.

You have sequenced a 100-kb region of the Bacillus anthracis genome (the bacterium that causes anthrax) and a 100-kb region from the Gorilla gorilla genome. What differences and similarities might you expect to see in the annotation of the sequences, for example, in the number of genes, gene structure, regulatory sequences, and repetitive DNA?

You have just obtained 100 kb of genomic sequence from an as-yet-unsequenced mammalian genome. What are three methods you might use to identify potential genes in the 100 kb? What are the advantages and limitations of each method?

When comparing genes from two sequenced genomes, how does one determine whether two genes are orthologous? What pitfalls arise when one or both of the genomes are not sequenced?

What is a reference genome? How can it be used to survey genetic variation within a species?