Staden: Using Patterns to Analyze Protein Sequences

Described here is one of the most powerful facilities provided by the program PIP: the ability to define and search sequences or libraries of sequences for complex patterns of motifs. Another chapter gives details of searching for individual motifs, but this chapter shows how to create individual patterns and libraries of patterns, and how to use them to search sequences. 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 against libraries of patterns routinely, this can be achieved by use of files of file names. For example, the program can use the PROSITE protein motif library. 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 a SWISSPROT feature table, or draw a simple graphical plot.