Staden: Using Patterns to Analyze Nucleic Acid Sequences

Abstract

Here is described one of the most powerful facilities provided by the program NIP: the ability to define and search for complex patterns of motifs (1–3). Chapter 8 gives details of searching for individual motifs, but this chapter shows how to create patterns and libraries of patterns, and to use them to search single sequences and sequence libraries. Once a pattern has been defined and stored in a file, it can be used to search any sequence. In addition, if users want to screen sequences routinely against libraries of patterns, this can be achieved by use of files of file names. The program can produce several alternative forms of output. It will display the segment of sequence matching each individual motif in the pattern, display all the sequence between and including the two outermost motifs, produce a description of the match in the form of an EMBL feature table, or draw a simple graphical plot.