Garlic Tutorial

Lesson 8 - Draw Averaged Hydrophobicity and Hydrophobic Moment

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.

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 or downloaded via ftp . Save this sequence as ASCII text, not as HTML.

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.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the sequence.

seq load sample.fasta

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).

plot hyd

Step 4 - plot the hydrophobic moment. Use mouse to identify residues.

plot mom

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!

plot hyd mom

Step 6 - return to the main drawing mode. You can either type the command plot off or hit the escape key.

plot off

Step 7 - clear the sequence buffer. You can skip this step, it is not very important.

seq reset