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<html>
<head>
<title>
Lesson 8
</title>
</head>
<h1 align=center>
Garlic Tutorial
</h1>
<h2 align=center>
Lesson 8 - Draw Averaged Hydrophobicity and Hydrophobic Moment
</h2>
<hr size="3">
In this lesson, you will learn how to draw the averaged hydrophobicity and
hydrophobic moment for the sequence which is stored in the main sequence
buffer.
<br><br>
In this lesson no atomic coordinates will be used. The only information
available will be the sample protein sequence stored in FASTA format.
The sample sequence may be found in the original garlic package.
Save this sequence as ASCII text, not as html.
<br><br>
In this example, mouse may be used to identify residues and their imminent
sequence neighborhood. The residue information will be visible in the
output window (bottom right corner), while the neighboring residues will be
listed in the upper part of the main window. The central residue (the one
choosen by the mouse) will be enclosed in a small rectangle.
<br><br>
Step 1 - start garlic (if not started already):
<br><br>
<font color=RED>
garlic
<br><br>
</font>
Step 2 - load the sequence.
<br><br>
<font color=RED>
seq load sample.fasta
<br><br>
</font>
Step 3 - plot the averaged hydrophobicity. Use mouse to identify the
residues in the plot. The residue information will be visible in the output
window (bottom right corner).
<br><br>
<font color=RED>
plot hyd
<br><br>
</font>
Step 4 - plot the hydrophobic moment. Use mouse to identify residues.
<br><br>
<font color=RED>
plot mom
<br><br>
</font>
Step 5 - plot both averaged hydrophobicity and hydrophobic moment.
Note that the numeric value in the output window will be equal to the
hydrophobic moment in this case!
<br><br>
<font color=RED>
plot hyd mom
<br><br>
</font>
Step 6 - return to the main drawing mode. You can either type the command
plot off or hit the escape key.
<br><br>
<font color=RED>
plot off
<br><br>
</font>
Step 7 - clear the sequence buffer. You can skip this step, it is not very
important.
<br><br>
<font color=RED>
seq reset
<br><br>
</font>
<hr size="3">
</html>
|
