Services
NetNES - 1.1
Leucine-rich nuclear export signals (NES) in eukaryotic proteins
The NetNES 1.1 server predicts leucine-rich nuclear export signals (NES) in eukaryotic proteins using a combination of neural networks and hidden Markov models.
Out of Commission
This service is unfortunately out of commission at this time.The software may still be available for download for academic institutions at the Downloads tab.
Instructions
1. Specify the input sequences
All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:
All the other symbols will be converted to A before processing. The sequences can be input in the following two ways:
-
Paste a single sequence (just the amino acids) or a number of sequences in
FASTA
format into the upper window of the main server page.
- Select a FASTA file on your local disk, either by typing the file name into the lower window or by browsing the disk.
Both ways can be employed at the same time: all the specified sequences will
be processed. However, there may be not more than 2,000 sequences
and 200,000 amino acids in one submission.
The sequences should not be shorter than 15
or longer than 7,000 amino acids.
2. Customize your run
The button labelled "Generate graphics" controls whether a graphical output of the prediction is created. By default it is on - click to turn off.3. Submit the job
Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.
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 - //
References
Analysis and prediction of leucine-rich nuclear export signals
Tanja la Cour, Lars Kiemer, Anne
Mølgaard, Ramneek Gupta, Karen Skriver
and Søren Brunak
Protein Eng. Des. Sel., 17(6):527-36, 2004.