HOW TO USE THE Predict 7 programme.

1. Save your amino acid sequence as e.g. tryp1.txt (a text file) onto a disc or flashdrive.
2. Double click on the Predict 7 programme.
3. The window asks for a file. You need to specify where the PfLDH.txt file is to be found
i.e. drive:\ folder\file. E.g. C:\tryp1.txt and your sequence should appear in the window (you
could also just drag the txt file over the Predict7 programmed and it will automatically open
Predict7 with the sequence loaded up).
4. Continue to press ENTER until a new page appears with the title “how do you wish to
get the results”
5. SELECT 6. OPTIONS
6. On “Options to change” screen SELECT 2 “Choose predictions to show”
7. Predictions include
1. Hydrophilicity
2. Hydropathy
3. Flexibility
4. Surface probability
5. Antigenicity
6. Secondary structure
7. Secondary structure N Glycosylation
8. SELECT 1,3,4,5 and then press ENTER
9. Press ESC and then 4 “Graph” to view a plot of the data.
10. For long sequences (>100): If a region of the plots “looks” promising. NOTE the numbers
of the amino acids
Press ESC, 6 Options, 3 range to show and select the range of amino acids to look at,
e.g. 1st amino acid type 50, Enter, last amino acid type 100, Enter. Press ESC, then 4
and look at that range. If you only have

Example of the plots shown on next page

 5
4
3
2
1 Series1
0
-1 1 14 27 40 53 66 79 92 105 118 131 144 157 170 183 196 209 222 235 248 261 274 287 300 313

-2
-3
-4

1.2

0.8

0.6 Series1

0.4

0.2

0
1 14 27 40 53 66 79 92 105 118 131 144 157 170 183 196 209 222 235 248 261 274 287 300 313

1.5

0.5
Series1
0
1 14 27 40 53 66 79 92 105 118 131 144 157 170 183 196 209 222 235 248 261 274 287 300 313
-0.5

-1

-1.5

0.2
0.15
0.1
0.05
0
-0.05 1 14 27 40 53 66 79 92 105 118 131 144 157 170 183 196 209 222 235 248 261 274 287 300 313 Series1
-0.1
-0.15
-0.2
-0.25
-0.3
 11. TO save your data. SELECT Option 3 – FILE and enter where you would like to save
the data. SAVE as tryp1data.txt on your flashdrive. The data will have been saved as a
text file.
12. TO plot the data separately. On the Text file copy the data for the 4 plots you analysed
and PASTE into an EXCEL file.
13. In the EXCEL file go to DATA and put the data into columns.
14. Highlight the amino acid number (or amino acid name) and then press the CHART icon
(at top) select a line chart and the first subtype.
15. Highlight the row marked HYDPK and get a copy of the graph.
16. Repeat for rows Log Flex, Surf and Agct.
17. You now have the same plots as you obtained in the programme.

Plotting the values obtained from Predict7, once imported into Excel
1) Minus 1 from the flexibility values to bring it onto a scale above and below zero.
Do this by copying the Flexibility values to a column to the right of the last column of
values. Enter a formula in the next column as follows: type in the first cell =; click on the 1st
Flexibility value and type -1; copy this formula down the Calculation column. Example of
Formula =E1-1 Copy all the values from the Calculation column and Paste special (Values
only) back into the original Flexibility column. Delete copy of Flexibility and Calculation
columns.

2) Plot hydrophilicity, surface probability, flexibility and antigenicity versus amino acid number.
The graph will look something like this…

Hydrophilicity Flexibility Surface probability Antigenicity

1.5

0.5

0
0 2 4 6 8 10 12 14 16
-0.5

-1
Amino acid number
3) Plot flexibility and antigenicity on a secondary Y axis. This is done by selecting the data
series on the graph (right click) – Format data series – Axis – select secondary axis. This has to
be done individually for flexibility and antigenicity. The graph will look something like this…

Hydrophilicity Surface probability Flexibility Antigenicity

1.5 0.15

1 0.1

0.05
0.5
0
0
-0.05
0 2 4 6 8 10 12 14 16
-0.5 -0.1

-1 -0.15
Amino acid number

4) Adjust maximum and minimum values on the Y-axes so that they are the same above and
below zero – this must be done on both Y-axes [e.g. 1.5 (or 0.15)above and below zero]. This
ensures that the zero values on the Y axes intersect.

Hydrophilicity Surface probability Flexibility Antigenicity

1.5 0.15

1 0.1

0.5 0.05

0 0
0 2 4 6 8 10 12 14 16
-0.5 -0.05

-1 -0.1

-1.5 -0.15
Amino acid number

5) The final touches include labelling your respective axes and moving the amino acid numbers
to the bottom of the graph – This is done by right clicking the primary Y axis – Format axis –
Adjust “value (X) axis, crosses at…” to your minimum value on the scale, i.e. -1.5 for the
example graph.
Give the chart a name [use the sequence name, e.g. Tryp1 (residues 1-16)]
 Tryp1 (residues 1-16)
Hydrophilicity Surface probability Flexibility Antigenicity

1.5 0.15

Hydrophilicity and surface

1 0.1

Flexibility and
0.5 0.05

antigenicity
probability 0 0
-0.5 -0.05

-1 -0.1
-1.5 -0.15
0 2 4 6 8 10 12 14 16
Amino acid number