Analyzing such similarities in fact provides clues into structure-function relationships and the mechanisms of molecular evolution in proteins. Aligning two or more sequences for comparison is an essential step in determining if they are homologous, and numerous procedures and computer programs are available for this purpose. The greatest complication in aligning sequences arises from allowances for insertion and deletion of amino acid residues to make an alignment work. The introduction of gaps in a sequence diminishes the significance of any alignment, so a penalty is usually assigned for each gap when assessing the significance of a given result.
Dynamic programming is the algorithm of basic sequence alignment for optimizing matches.
Physical and chemical properties of amino acids have to be considered in assessing similarities and differences, as closely related proteins demonstrate when chemically similar aminoacids most often replace each other in substitution mutations. The first step in protein alignment is the retrieval of the sequences to be compared. The most common approach is by description or identification, i.e. by filling in the common name of the protein of interest, then choosing among the several matches. Saving these results as text only, files are ready for further use. Freeware and shareware alignment software is available, but we prefer on-line programs, accessible through the World Wide Web.