JaMBW Chapter 3.1.2
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:
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:
- 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.
- 12 colors are used, which are given to the various features, using mod 12 of the checksum from the name of the feature. In this
way if multiple applets are present on the same page, the features will have the same color.
- bubble sort is used for sorting the features alphabetically, so that if multiple copies of the applet are present the user will find
the features in a easy (mnemonical) way.
- overlapping entries on the same feature are not recognizable by color.
- 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.
- 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
<applet code=FeatureTable.class width=800 height=200>
<param name=ID value=GHR_PIG>
<param name=RAW value=MDLWQLLLTLAVAGSSDAFSGSEATPAVLVRASQSLQRVHPGLETNSSGKPKFTKCRSPELETFS>
<param name=FT value=SIGNAL+1+18+something|CHAIN+19+638+GROWTH_HORMONE_RECEPTOR|DOMAIN+9+264+EXTRACELLULAR_(POTENTIAL)|>
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.
- European Bioinformatic Institute(1996) DDBJ/EMBL/GenBank Feature Table Definition, v1.09.
Author:Luca I.G. TOLDO,
Edition date: 28 February 1997