Bioinformatics: Sequences, Codes, and Evolutionary Concepts

Vocabulary flashcards reviewing core bioinformatics definitions, IUPAC one-letter nucleotide codes, and mutational terminology.

Genome

The entire complement of genetic material carried by an individual.

Transcriptome

The entire set of transcribed sequences produced by the genome.

Proteome

The entire set of proteins encoded by the genome.

Similarity

The observed resemblance between two characters.

Homology

The condition of two traits being derived (with or without modifications) from a common ancestor.

Mutation

An error in the replication of the nucleotide sequence encompassing one or more nucleotides (and in complicated situations, disjoint nucleotides), caused by internal errors of metabolism or external agents such as radiation.

Substitution

Differences in two sequences that originally arose by mutations but have been acted upon by natural selection.

Replacement

Observed differences between amino acid sequences.

Transition

A nucleotide change from a purine to a purine ($\text{purine} \rightleftharpoons \text{purine}$) or from a pyrimidine to a pyrimidine ($\text{pyrimidine} \rightleftharpoons \text{pyrimidine}$).

Transversion

A nucleotide change from a purine to a pyrimidine ($\text{purine} \rightleftharpoons \text{pyrimidine}$) or from a pyrimidine to a purine ($\text{pyrimidine} \rightleftharpoons \text{purine}$).

Transition vs. Transversion Count

In DNA sequences, there are $8$ possible transversions for every $4$ possible transitions.

Purine (one-letter code R)

The single-letter ambiguity code denoting either Guanine ($\text{G}$) or Adenine ($\text{A}$).

Pyrimidine (one-letter code Y)

The single-letter ambiguity code denoting either Cytosine ($\text{C}$) or Thymine ($\text{T}$).

Amino base (one-letter code M)

The single-letter ambiguity code denoting an amino-containing base, either Adenine ($\text{A}$) or Cytosine ($\text{C}$).

Keto base (one-letter code K)

The single-letter ambiguity code denoting a keto-containing base, either Guanine ($\text{G}$) or Thymine ($\text{T}$).

Strong base (one-letter code S)

The single-letter ambiguity code denoting bases that form $3\text{ H}$ bonds, either Guanine ($\text{G}$) or Cytosine ($\text{C}$).

Weak base (one-letter code W)

The single-letter ambiguity code denoting bases that form $2\text{ H}$ bonds, either Adenine ($\text{A}$) or Thymine ($\text{T}$).

Not G (one-letter code H)

The single-letter ambiguity code representing any base other than Guanine ($\text{A}$, $\text{T}$, or $\text{C}$).

Not A (one-letter code B)

The single-letter ambiguity code representing any base other than Adenine ($\text{G}$, $\text{C}$, or $\text{T}$).

Not T (one-letter code V)

The single-letter ambiguity code representing any base other than Thymine ($\text{A}$, $\text{G}$, or $\text{C}$).

Not C (one-letter code D)

The single-letter ambiguity code representing any base other than Cytosine ($\text{A}$, $\text{G}$, or $\text{T}$).

Any base (one-letter code N)

The single-letter ambiguity code representing any standard nucleotide ($\text{G}$, $\text{C}$, $\text{T}$, or $\text{A}$).

Unknown base (one-letter code X)

The single-letter ambiguity code representing an unknown nucleotide base ($\text{?}$).