JaMBW Chapter 4.1

Pattern search


Given a sequence of nucleic acids or amino acids, and the description of one or more binding sites or restiction sites, this program reveals their occurrence in graphical and tabular ways. Examples of this application are:

Mode of operation

This program uses 3 windows for obtaining information about the sequence to analyze and the pattern(s) to use, and returns the results of its operations in graphical, textual and tabular way. The following steps must be performed in order to use it:
  1. Sequence
  2. Pattern

    In this distribution are included the following pattern files:

  3. Compute
    Once the parameters have been chosen, by pressing the "COMPUTE" button, then the patterns are searched and the sites found are displayed on a clickable chart.

A Java-enabled browser would have in this place a window similar to this picture:

How to understand its output

The graphical and clickable interface, with the optional tabular output, makes this program extremely intuitive to use. The bar chart is a pictorial representation of the location of specified patterns/binding sites across the sequence, which runs horizontally.The patterns are listed alphabetically from top to bottom, and colored randomly using 12 different colors. Infact, two different patterns might be shown using the same color. This should not confuse the user, which should use the name of the pattern as identifier. Clicking on a colored bar induces the display of further information on that specific result, which are shown in the textual part of the applet, running in the bottom of the chart.
The table that is generated upon selecting the "Print/List" button, is useful for storing the results in on paper and for further reference. It contains the same results as shown in the graph, with the patterns found listed alphabetically descending, and for each pattern giving the location of the site, in units from the beginning of the sequence.


Author:Luca I.G. TOLDO, Edition date: 28 February 1997