IMP GPI Lipid Anchor Project IMP-Bioinformatics

How to read the prediction results: learning and mutation data sets

Contact:
Birgit Eisenhaber (MDC/IMP)
Peer Bork (MDC/EMBL)
Frank Eisenhaber (IMP)


Examples of prediction results

Example 1
18.95 0.00 0.00 -0.21 0.00 0.00 0.00 0.00 0.00 -0.23 -0.17 0.00 0.00 0.00 0.00 0.00 18.34
ID: G13B_DICDI AC: P34116 Len: 734 1:B 708 Sc: 18.34

Example 2
23.88 -0.63 -0.91 -0.53 0.00 0.00 0.00 0.00 -0.76 -0.17 -0.31 0.00 0.00 0.00 0.00 0.00 20.58
ID: VSI3_TRYBB AC: P26328 Len: 532 1:B 509 Sc: 20.58
$ site was 511

Example 3
28.10 -0.57 -0.83 -0.72 0.00 0.00 0.00 -0.85 -0.34 -2.54 -5.29 -12.00 0.00 0.00 -12.00 0.00 -7.06
ID: VSG4_TRYBR AC: P02897 Len: 476 1:I 457 Sc: -7.06

Example 4
4.25 0.00 0.00 0.00 0.00 0.00 -8.00 0.00 0.00 -2.79 -0.61 -12.00 -12.00 0.00 -12.00 0.00 -43.15
ID: DAF_HUM_D1 AC: C50002 Len: 364 1:I 349 Sc: -43.15 Pv: 1.565512e-01

Explanation of the prediction results

The first line of the prediction result represents the components of the score function for the potential omega-site position having the highest score for the query sequence.
The first number is the total profile score calculated for the sequence regions described in the parameter section of the program output (see previous page). In the example 1 (G13B_DICDI), the profile value is 18.95.
The following 15 numbers show the values for the terms Function0 .. Function14 (see previous page) separately. In example 1, the value for Function8 which evaluates the average hydrophobicity of the hydrophobic tail is -0.23.
The last number shown in bold is the total score - the highest score for the best potential omega-site position.

The second line is the result line. The image refers to correct predicted entries (examples 1, 2 and 4), the image to false predicted (example 3). Some informations about the entry are given (here entry name, accession number, sequence length).
This part is followed by the prediction of the best omega-site, its quality (A,B,C,D, or S for potential sites, I or N for no site), the best omega-site position and the associated total score and, except for the learning set, P-value (derived from an extreme value distribution).

In the case of the self-consistency-test of the learning set, the correctness of the predicted omega-site is proved. The third line will occur, if the predicted site differs from the annotated site. In the example 2 (VSI3_TRYBB), the annotated GPI modification site was at position 511, the prediction function found it at position 509.


Last modified: 13th June 2002