DNA Base Composition Analysis Tool

Introduction

This analysis tool can analysis a DNA sequence in three different ways. It computes the percentage of one or two selectable nucleotide(s), the normal skew of two selectable nucleotides, and the cumulative skew of two selectable nucleotides for a given sequence. The result can be displayed in both graph and value data format.

For the computation the genome is separated into parts, which called windows. The windows are shifted along the sequence by a certain step size. The percentage or skew value is calculated for every window.

For percentage calculation, the user can choose one or two nucleotide(s), the value of percentage is computed by the formula:
      Percentage = nucleotide / (A + C + G + T)
            (for one selected nucleotide) or
      Percentage = (nucleotide1 + nucleotide2) / (A + C + G + T)
            (for a pair of different nucleotides)

For skew calculation, the user should choose a pair of different nucleotides. The skew values are computed by the formula:
      Skew = (nucleotide1 - nucleotide2) / (nucleotide1 + nucleotide2)

The normal skew value relates to the particular position in sequence. The cumulative skew value adds up the values for all previous windows up to the certain position.

The global minimum, maximum, and average values are shown in the percentage computing result.

The global minimum and maximum values and positions of sequence are shown in the normal and cumulative skew computing result.

The minimum and maximum value of a GC-skew can be used to predict the origin of replication (minimum) and the terminus location (maximum) in procaryotic genomes.

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System Requirements

The program was implemented by Java 1.1 and compiled by JDK1.1.6. Therefore, the program should run correctly in any web browsers that support Java 1.1.6.

The program has been tested in Internet Explore 6.0 (Window, Mac and Unix system), Netscape 4.7 (Window), Netscape 7.0 (Window, Unix, Mac) and Safari (Mac).

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Requirement of input data

DNA Sequence Name
You can give your DNA sequence name here. This name will be shown in the title of graph.
Sequence
You should paste your DNA sequence for analysis here. The sequence is only allowed containing nucleotides: A, C, G, T and N.
Analysis Type
You can select one of the three analysis types for your DNA analysis. For percentage analysis, your can choose one or two nucleotide(s). If the two nucleotides are same, the one nucleotide percentage of the given sequence will be calculated. For skew analysis, you must choose two different nucleotides.
Window and Step Setting
When you increase the window size and decrease the step size, you will get more significant values. But in the meantime, the calculating time will be longer depending on the capacity of your computer. Therefore, the window and step size are limited.

The size for both window and step must be larger than the length of sequence divided by 10000. If you do not give the size of window or step, or give the negative values, the window and step size will be set one by default and follow the restricted size rule.

If there are any errors of input, the message will be shown after you click "Run Analysis" button.
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How can I run analysis?

When you input the required data or change the settings of calculation, please click button. The program will show the analysis result in a graphic format.
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How to view data value result?

Click button, the program will show the computing data value. When you click button, then the computing result will be shown in graphic.
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Can I change the color of graphic curve?

Yes. There are three options, blue, green, red, for curve color. By default, the graphic is drawn in blue color. Click the color button , the curve will be drawn in the corresponding color.
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What does the average button use for?

In percentage calculation, the global average will be computed. By click button, the program will draw the average line in the graph if there is no average line or erase the average line if there is average line in graph.
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How to save the results?

For saving graphic, you can click "Print Screen" key in the keybroad to make a screen snap. Then, open any graphic editor, such as Window Paint, Paintshop, or Adobe Photoshop, and choose "paste" in edit menu to paste the screen snap in the graphic editor. By editing the screen snap picture, you can get the graphic of DNA analysis result.

For saving the value data, you can select all value data by click button when the program shows computing value data result. By right-click and select "copy" to copy the data, then go to any text editor, you can paste the data and save them in a text file.

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