By relating a score S to the expected distribution it is possible to calculate a p value which indicates the probability that the specified score could occur by chance. Thus p values close to zero are the most significant. The smaller the value of E the more statistically significant the alignment. F. Database Searching Pairwise sequence alignments can be extended such that one sequence becomes the query sequence and any of the sequneces in a database become a target sequence to determine a large set of pairwise alignments. To scale computationally either parallel computation is needed or heuristic methods.
Heuristic methods make assumptions at the risk of missing some alignments.
Both protein and DNA sequences contain low-complexity regions and DNA sequences in particular contain repetative elements. Filtering attempts to remove the confusion such regions can cause to a database search. This can be done either by first checking the query sequence or filtering the results.