[27] Local alignment statistics

This chapter discusses the study of local alignment statistics, the distribution of optimal gapped subalignment scores, and the evidence that two parameters are sufficient to describe both the form of this distribution and its dependence on sequence length. Using a random protein model, the relevant statistical parameters are calculated for a variety of substitution matrices and gap costs. An analysis of these parameters elucidates the relative effectiveness of affine as opposed to length-proportional gap costs. Thus, sum statistics provide a method for evaluating sequence similarity that treats short and long gaps differently. By example, the chapter shows how this method has the potential to increase search sensitivity. The statistics described can be applied to the results of fast alignment (FASTA) searches or to those from a variation of the basic local alignment search tool (BLAST) programs.