Staden: Searching for Motifs in Nucleic Acid Sequences

The program NIP contains several ways of defining and searching for motifs (1 –4 ), and also contains a number of “hardwired” motifs that are already defined and can be selected as separate searches. Searches for percentage matches to consensus sequences, the use of score matrices, and the creation and use of nucleotide and dinucleotide weight matrices (see Note 7) are described here. In addition, details are given of the “hardwired” motifs available from the program. Chapter 6 has covered searches for exact matches to consensus sequences by describing how to find restriction enzyme recognition sequences. When searching for exact matches, percentage matches, or using a score matrix the search string or consensus sequence may include IUB redundancy codes. All of the searches produce both listed and graphical output. The listed output displays the matching sequence and its position, and the graphical output draws a box to represent the length of the sequence and plots vertical lines within the box at the positions of matches. The heights of the lines are proportional to the match score (see Fig. 1 ).