The programs are not generally useful for motif-style searching. In the programs described here, Karlin-Altschul statistics have been extrapolated to the task of assessing the significance of .SM HSP scores obtained from comparisons of potentially short, biological sequences. T when aligned with a word of the same length in a database sequence. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. E establishes a statistical significance threshold for reporting database sequence matches.
E is subject to being reported in the program output.
W , which severely reduces the program's sensitivity but provides for high speed searches. W has any value other than 3 or 4. Any letter which is not a member of this alphabet will be stripped from an amino acid query sequence on input and will not contribute to the query sequence coordinate numbers displayed in program output. In protein sequence databases that are processed into searchable form by the .BR setdb program, any non-alphabetic letters are also stripped. N parameters, the scoring matrix constructed by the program accounts for partial matching of nucleotide ambiguity codes.