6 Glossary

Alignment:

A biologically similar region between two sequences.

Frame number:

The frame number determines the way a DNA sequence is translated into a protein sequence-the 1st, 2nd, or 3rd nucleotide of the positive strand of the DNA sequence, or the 1st, 2nd, or 3rd nucleotide of the negative strand.

Nucleotide:

An element of a DNA sequence, sometimes also called a base.

PAM distance:

Point-Accepted Mutations is a measure of evolutionary distance, which is a rough measure of how many generations of evolution it would take to mutate one sequence into another.

Similarity Score:

A measure of the amount of similarity in an alignment. It is the sum of all residue pair scores in an alignment.

Substitution matrix:

A two dimensional matrix representing the likelihood of one amino acid replacing another. These matrices are the foundation of statistical techniques for finding alignments.

Residue:

An amino acid, which is a basic element in a protein sequence.

Residue Pair Score:

An entry in a substitution matrix.