Studies of varying alignment algorithm, amino Acid scoring matrix, and gap penalties

INTRODUCTIONComparing different amino acid scoring matrix-gap penalty combinations poses several problems. For example, the analysis often overlooks the purposes of different matrices; e.g., protein family or domain searching, evolutionary analysis, or structural alignment. In the past, gap penalties were usually not published or well known, thus throwing a level of uncertainty into the results. More recently, when investigators publish a new scoring matrix, they usually provide suitable choices for gap penalties that may be used for comparisons with other matrices. This article summarizes a number of reports that have examined combinations of alignment algorithm, scoring matrix, and gap penalties used to align sequences for various purposes.