NetGPI - 1.0

This version of NetGPI has been discontinued. Please use the most recent version of NetGPI

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:

A C D E F G H I K L M N P Q R S T V W Y and X (unknown)

All the alphabetic symbols not in the allowed alphabet will be converted to X before processing. All the non-alphabetic symbols, including white space and digits, will be ignored.

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 5,000 sequences in one submission. The sequences may not be longer than 10,000 amino acids.

2. Customize your run

Generating figures for a large number of samples takes much longer than executing a prediction. Consider using the short option for large sample batches.

• Output format:
  You can choose between two output formats:

  Long

  Appropriate for most users. Shows one plot and one summary per sequence.

  Short

  Convenient if you submit lots of sequences. Shows only one line of output per sequence and no graphics.

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.

Example Outputs

By default the server produces the following output for each input sequence. The example below shows the output for intestinal-type alkaline phosphatase 1, taken from the Uniprot entry PPBI1_RAT. The lipidation position prediction is consistent with the database annotation.

One annotation is attributed to each protein, the one that has the highest probability. If the highest probability is within the amino-acid sequence, then it is considered GPI-anchored and the amino-acid position at the peak is the predicted omega-site. If the highest probability is at the sentinel, here represented by *, then the protein is considered non GPI-anchored.

If a GPI-anchor is predicted, the omega-site position is reported as well.

On the plot we see the likelihood distribution over the protein sequence, with the added sentinel *. Only the last 100 amino-acids are considered.

Example: Mature protein - standard output format

Training and testing data sets

The datasets for training and testing NetGPI-1.0 can be found here. Both datasets are in 2-line FASTA format.

The training/validation header is as follows:

>Uniprot_AC|anchoring|pos_from_end|pos_from_beginning|part_no
amino-acid sequence

where:

• Uniprot_AC is an accession number
• anchoring is GPI-anchored or non_GPI-anchored
• pos_from_end is the position within the sequence from the end, where 0 is the sentinel
• pos_from_beginning is the position within the truncated sequence from the beginning
• part_no is the partition that the protein belongs to

The test hearder is as follows:

>Uniprot_AC|anchoring|pos_from_end|pos_from_beginning|exp_verified
amino-acid sequence

where:

• Uniprot_AC is an accession number
• anchoring is GPI-anchored or non_GPI-anchored
• pos_from_end is the position within the sequence from the end, where 0 is the sentinel
• pos_from_beginning is the position within the truncated sequence from the beginning
• exp_verified is 1 if the omega-site has been experimentally verified, 0 otherwise

Training/Validation set: download

Benchmark set: download