JaMBW Chapter 3.1.2

Feature Viewer


Given a sequence and the features which are annotated in its sequence, this program produces a visual display which allows to tightly interact with features, sequence and access at the full text of the specified feature.

Mode of operation

The program uses three output areas:
  1. graphical view of each feature
    The features contained in a sequence are colored using the same color and are located along the same bar, which runs for the whole length of the sequence.

  2. textual description of the selected feature
    Upon clicking on a feature the textual information associated with it is displayed in the textual area below the bar chart.

  3. graphically enhanced view of the sequence
    Upon clicking on a feature the sequence is colored with the same color of the feature and this colored view of the sequence is returned in the bottom panel
This applet had been designed in conjunction with the SRS5 service, in order to allow graphical view of sequences, with special emphasis on the highly informative content associated in the annotated features. To include this applet in your page, do as follows:
<applet code=FeatureTable.class width=800 height=200>
<param name=ID value=GHR_PIG>

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

How to understand its output

The entirely graphical and clickable interface, with absence of parameters to be selected by the user, makes this program extremely intuitive to use. The bar chart is a colored representation of the location of features across the sequence, which runs horizontally. The vertical yellow lines are drawn at 10 bases/aminoacids interval. In fact, this program can be used both for nucleic acid as well as for amino acid sequences.


  1. European Bioinformatic Institute(1996) DDBJ/EMBL/GenBank Feature Table Definition, v1.09. http://www.ebi.ac.uk/ebi_docs/embl_db/ft/introduction.html

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