Practice Quiz 1

A retrotransposon differs from Tc1/mariner in that it

moves through an RNA intermediate (copy-and-paste)

A GFF3 file records the Tc1 transposase as two CDS rows spanning 201–400 and 501–1300. Coordinates are 1-based and inclusive. How many base pairs of coding sequence is that

1000

An alignment column contains all four bases in equal proportion (25% each). Against a uniform 4-base background, how much information does that column carry

0 bits

Two Tc1 copies in one host genome arose by a recent duplication within that species. They are best described as

Paralogs

Why is “just take the commonest base among the leaves” an unreliable way to reconstruct an ancestor

he leaves are not independent — a cluster of close relatives can outvote a lone deep branch

Tc1-like element keeps both of its TIRs but its transposase gene has been broken by a deletion. What is the most common way such a non-autonomous element still moves

transposase made by an autonomous copy elsewhere in the genome acts on its TIRs

ou have a Tc1 element as a FASTA file and want to record where its TIRs and transposase CDS lie. Which format is designed to store those feature coordinates

GFF

In a DNA sequence logo, the total height of the stack of letters above one column represents:

The column’s information content R in bits — at most 2 bits for DNA

You are handed an unrooted tree whose tips are Tc1 copies found in present-day genomes. Which question can it not answer

CANT show which copies are ancestral to which, since it carries no direction of time

Parsimony reconstruction of an ancestral state chooses the state that

Requires the fewest substitutions to explain the leaves

An autonomous Tc1 element is organised as

one transposase gene flanked by two terminal inverted repeats

A collaborator sends you X01005.gff3, whose rows are all feature lines, and nothing else. To pull out the transposase’s nucleotide sequence you also need

The FASTA file holding the sequence named in the seqid column

In a sequence logo built from several Tc1 copies, the TIR columns and the duplicated TA target site stand at nearly 2 bits, while the columns further out in the flanking genomic DNA are close to 0 bits. Those near-zero columns mean that

he flanking bases vary freely from copy to copy, so none is predictable

In Newick format each pair of parentheses groups the copies descending from one internal node, so (((c1,c2),c3),c4); relates four Tc1 copies. A clade is an ancestor together with all of its descendants. Which group is a clade of this tree

c1, c2 and c3

Besides the aligned present-day sequences, what does maximum likelihood ancestral reconstruction require

a tree with branch lengths, plus a substitution model for base changes along a branch

The transposase that mobilises Tc1/mariner is catalytically a

DDE enzyme, named for its catalytic triad. AspAspGln

In the Tc1 GFF3 the transposase row carries the attributes ID=tpase;Parent=Tc1. What does the Parent attribute record

hat this CDS is a subfeature of the element whose ID is Tc1

In R = log₂ 4 − H, what does the log₂ 4 term stand for

The entropy of the uniform “know-nothing” background over the 4 bases

On a tree of Tc1 copies, a long branch leading to one copy means that:

many substitutions have accumulated along that lineage

An ancestral node has two descendant leaves: one on a very short branch reading A, the other on a very long branch reading G. Maximum likelihood reconstructs the ancestor as:

A, since a substitution is far less likely on the short branch than on the long one