Book: "Bioinformatics Sequence and Genome Analysis"

Affine gap penality is a gap penality score that is a linear function of gap length, consisting of a gap opening penality and a gap extension penality multiplied by the length of the gap.

Alignment score is a computed score based on the number of matches, substitutions, and insertions/deletesions (gaps) within an alignment. For DNA sequences, usually a match and mismatch score is chosen along with a gap penality that will produce the most reasonable alignment.

BLOSUM scoring matrices are commonly used to align protein sequences.

Convergent evolution refers to the evolution of two genes to the same biological function. However, because they have different starting points, the resulting sequences are not similar.

Distance score between aligned sequences is a measure of the evolutionary distance between the sequences.

Dynamic programming algorithm solves the problem of finding the optimal alignment between sequences by breaking the alignment down into a series of sequential sub-alignments that can be readily computed.

PAM scoring matrix, or percent accepted mutation scoring matrix, is a table or matrix that describes the odds that a sequence position, e.g., an amino acid, has changed into a second one during a period of evolutionary time.

Smith-Waterman algorithm is a dynamic programming algorithm for locating the highest-scoring local alignments of sequences. The key feature is that all negative scores calculated in the dynamic programming matrix are changed to zero to avoid extending poorly scoring alignments and to assist in identifying local alignments starting and stopping anywhere in the matrix.

In a local alignment, the alignment stops at the ends of regions of strong similarity, and a much higher priority is given to finding these local regions than to extending the alignment to include more neighboring amino acid pairs.

Odds ratio in the sequence alignment is the ratio of the odds o f obtaining the sore of related sequences to the odds of obtaining the same score between unrelated sequences.