NetNES 1.1 Output format

Output format

DESCRIPTION

Providing 'Generate graphics' is enabled, server output consists of two parts; one is a listing of all residues with the indiviual scores noted (see column heading), the other is a graphical plot of the values given in the first table. If 'Generate graphics' is deselected the plot will be omitted.

As described in the paper, the prediction server calculates the NES score from the HMM and Artificial Neural Network (ANN) scores but all three values are given for each residue. This allows for manual inspection of possible mispredictions. A wrong prediction is sometimes obtained because either the HMM or the ANN fails to recognize the NES motif completely. In that case an experienced user might be able to spot that from the individual scores.

Even though the ANN is trained to specifically recognize the last (most C-terminal) hydrophobic position of the NES motif, it is often seen that the other hydrophobic positions give rise to peaks in the ANN score. Again, the experienced user might benefit from the additional information in the ANN score and be able to rescue a misprediction.

In summary, if the calculated score 'NES score' exceeds the threshold, then that particular residue is expected to participate in a nuclear export signal. This is denoted with a 'Yes' in the column 'Predicted'.

Note that non-standard amino acid abbreviations (BJOUXZ) are replaced with alanines.

For further information, please refer to the publication or contact us.

EXAMPLE OUTPUT

>REV_HV1C4 - netNES 1.1 prediction #Seq-Pos-Residue ANN HMM NES Predicted #--------------------------------------------------------- REV_HV1C4-1-M 0.121 0.000 0.000 - REV_HV1C4-2-A 0.081 0.000 0.000 - REV_HV1C4-3-G 0.109 0.000 0.000 - REV_HV1C4-4-R 0.089 0.000 0.000 - REV_HV1C4-5-S 0.097 0.000 0.000 - REV_HV1C4-6-G 0.096 0.000 0.000 - REV_HV1C4-7-D 0.090 0.000 0.000 - REV_HV1C4-8-S 0.084 0.000 0.000 - REV_HV1C4-9-D 0.087 0.000 0.000 - REV_HV1C4-10-E 0.125 0.000 0.000 - REV_HV1C4-11-E 0.078 0.000 0.000 - REV_HV1C4-12-L 0.168 0.000 0.000 - REV_HV1C4-13-I 0.086 0.000 0.000 - REV_HV1C4-14-K 0.096 0.000 0.000 - REV_HV1C4-15-T 0.098 0.000 0.000 - REV_HV1C4-16-V 0.094 0.000 0.000 - REV_HV1C4-17-R 0.114 0.000 0.000 - REV_HV1C4-18-I 0.193 0.000 0.000 - REV_HV1C4-19-I 0.101 0.000 0.000 - REV_HV1C4-20-K 0.081 0.000 0.000 - REV_HV1C4-21-H 0.236 0.000 0.000 - REV_HV1C4-22-L 0.445 0.000 0.234 - REV_HV1C4-23-Y 0.094 0.000 0.000 - REV_HV1C4-24-Q 0.097 0.000 0.000 - REV_HV1C4-25-S 0.071 0.000 0.000 - REV_HV1C4-26-N 0.069 0.000 0.000 - REV_HV1C4-27-P 0.093 0.000 0.000 - REV_HV1C4-28-P 0.087 0.000 0.000 - REV_HV1C4-29-P 0.070 0.000 0.000 - REV_HV1C4-30-K 0.064 0.000 0.000 - REV_HV1C4-31-P 0.070 0.000 0.000 - REV_HV1C4-32-E 0.067 0.000 0.000 - REV_HV1C4-33-G 0.066 0.000 0.000 - REV_HV1C4-34-T 0.069 0.000 0.000 - REV_HV1C4-35-R 0.076 0.000 0.000 - REV_HV1C4-36-Q 0.082 0.000 0.000 - REV_HV1C4-37-A 0.087 0.000 0.000 - REV_HV1C4-38-R 0.074 0.000 0.000 - REV_HV1C4-39-R 0.070 0.000 0.000 - REV_HV1C4-40-N 0.075 0.000 0.000 - REV_HV1C4-41-R 0.077 0.000 0.000 - REV_HV1C4-42-R 0.077 0.000 0.000 - REV_HV1C4-43-R 0.081 0.000 0.000 - REV_HV1C4-44-R 0.087 0.000 0.000 - REV_HV1C4-45-W 0.087 0.000 0.000 - REV_HV1C4-46-R 0.075 0.000 0.000 - REV_HV1C4-47-E 0.086 0.000 0.000 - REV_HV1C4-48-R 0.087 0.000 0.000 - REV_HV1C4-49-Q 0.072 0.000 0.000 - REV_HV1C4-50-R 0.079 0.000 0.000 - REV_HV1C4-51-R 0.072 0.000 0.000 - REV_HV1C4-52-I 0.101 0.000 0.000 - REV_HV1C4-53-H 0.075 0.000 0.000 - REV_HV1C4-54-S 0.077 0.000 0.000 - REV_HV1C4-55-I 0.086 0.000 0.000 - REV_HV1C4-56-S 0.075 0.000 0.000 - REV_HV1C4-57-A 0.081 0.000 0.000 - REV_HV1C4-58-W 0.075 0.000 0.000 - REV_HV1C4-59-L 0.098 0.001 0.000 - REV_HV1C4-60-L 0.138 0.003 0.000 - REV_HV1C4-61-S 0.080 0.003 0.000 - REV_HV1C4-62-T 0.084 0.003 0.000 - REV_HV1C4-63-C 0.136 0.003 0.000 - REV_HV1C4-64-L 0.301 0.006 0.000 - REV_HV1C4-65-G 0.105 0.006 0.000 - REV_HV1C4-66-R 0.100 0.006 0.000 - REV_HV1C4-67-S 0.078 0.006 0.000 - REV_HV1C4-68-A 0.081 0.006 0.000 - REV_HV1C4-69-E 0.145 0.006 0.000 - REV_HV1C4-70-P 0.086 0.006 0.000 - REV_HV1C4-71-V 0.074 0.022 0.000 - REV_HV1C4-72-P 0.072 0.022 0.000 - REV_HV1C4-73-L 0.092 0.381 0.091 - REV_HV1C4-74-Q 0.086 0.380 0.091 - REV_HV1C4-75-L 0.110 0.998 0.702 Yes REV_HV1C4-76-P 0.070 0.996 0.696 Yes REV_HV1C4-77-P 0.082 0.996 0.698 Yes REV_HV1C4-78-L 0.108 0.996 0.705 Yes REV_HV1C4-79-E 0.073 0.995 0.701 Yes REV_HV1C4-80-R 0.234 0.995 0.731 Yes REV_HV1C4-81-L 0.179 0.995 0.745 Yes REV_HV1C4-82-T 0.113 0.977 0.735 Yes REV_HV1C4-83-L 0.872 0.977 1.310 Yes REV_HV1C4-84-D 0.081 0.000 0.000 - REV_HV1C4-85-C 0.292 0.000 0.000 - REV_HV1C4-86-S 0.091 0.000 0.000 - REV_HV1C4-87-E 0.106 0.000 0.000 - REV_HV1C4-88-D 0.169 0.000 0.000 - REV_HV1C4-89-C 0.103 0.000 0.000 - REV_HV1C4-90-G 0.096 0.000 0.000 - REV_HV1C4-91-T 0.090 0.000 0.000 - REV_HV1C4-92-S 0.105 0.000 0.000 - REV_HV1C4-93-G 0.088 0.000 0.000 - REV_HV1C4-94-T 0.079 0.000 0.000 - REV_HV1C4-95-Q 0.077 0.000 0.000 - REV_HV1C4-96-G 0.073 0.000 0.000 - REV_HV1C4-97-V 0.069 0.000 0.000 - REV_HV1C4-98-G 0.075 0.000 0.000 - REV_HV1C4-99-S 0.087 0.000 0.000 - REV_HV1C4-100-P 0.072 0.000 0.000 - REV_HV1C4-101-Q 0.068 0.000 0.000 - REV_HV1C4-102-I 0.116 0.000 0.000 - REV_HV1C4-103-L 0.078 0.000 0.000 - REV_HV1C4-104-V 0.076 0.000 0.000 - REV_HV1C4-105-E 0.087 0.000 0.000 - REV_HV1C4-106-S 0.076 0.000 0.000 - REV_HV1C4-107-P 0.080 0.000 0.000 - REV_HV1C4-108-A 0.077 0.000 0.000 - REV_HV1C4-109-V 0.108 0.000 0.000 - REV_HV1C4-110-L 0.085 0.000 0.000 - REV_HV1C4-111-E 0.079 0.000 0.000 - REV_HV1C4-112-S 0.120 0.000 0.000 - REV_HV1C4-113-G 0.071 0.000 0.000 - REV_HV1C4-114-T 0.072 0.000 0.000 - REV_HV1C4-115-K 0.097 0.000 0.000 - REV_HV1C4-116-E 0.077 0.000 0.000 - //

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