Pairwise Alignment, Multiple Alignment, and BLAST

Abstract

Quantitative comparison of sequences can be performed pairwise by aligning two sequences based on considerations of gaps representing insertions or deletions and matches between nucleotides and amino acids. Pairwise comparisons can be performed as global alignments if it is known that the sequences are homologous in their full length or by local alignments if it is known that one sequence is shorter than the other. The dynamic programming algorithms for constructing global and local alignments will be described in detail and relevant computer programs suggested. The different strategies behind multiple alignments are described including relevant computer programs. The search program BLAST is introduced in detail and different applications described.