Cite as: Cold Spring Harb. Protoc.; 2008; doi:10.1101/pdb.ip60

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Studies of Varying Alignment Algorithm, Amino Acid Scoring Matrix, and Gap Penalties

David W. Mount

Adapted from "Alignment of Pairs of Sequences," Chapter 3, in Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2004.


INTRODUCTION

Comparing 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.


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