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Usage 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 other symbols will be converted to X 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 maximal allowed sequence length is 4000 amino acids.

TargetP predictions are based on the 130 N-terminal residues of each input sequence. Therefore, it is strongly recommended to include the N-terminus for all sequences; missing N-terminal residues make the prediction more difficult and less reliable. Submitting more than 130 residues does not influence the prediction in any way (apart from making it slower).

The sequence names may be of any length, a maximum of 30 characters is preserved throughout the prediction. However, the special characters in the names (e.g. ";" and ">") will be changed into "_" (underscore) for technical reasons.

2. Customize your run

  • Organism group:
    Choose the TargetP version that corresponds to the origin of your data. Non-plant version predicts the locations mitochondrion, secretory pathway, and other. Plant version can also predict chloroplast as a possible location.

  • Prediction scope:
    For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted. If that is needed check the box labelled 'Perform cleavage site predictions'. ChloroP and SignalP are used for prediction of cTP and SP cleavage sites, respectively.

  • Cutoffs:
    By default no cutoff is used, the prediction is a "winner-takes-all". In order to increase specificity it might be useful, in addition, to impose restrictions on the prediction by demanding the score for a prediction not only to be the highest among the output scores, but also to be above a cutoff.

    Two predefined sets of cutoffs are provided, corresponding to specificities of 0.95 and 0.90, respectively (measured on the TargetP test sets). The user may also set own cutoffs; they should be between 0.00 and 1.00 (the range of the output values). Choosing specificity >0.95 or >0.90 implies automatically the use of the following cutoffs:

    Category Cutoff
        Plant     Non-plant
    0.95 cTP 0.73 -
    mTP 0.86 0.78
    SP 0.43 0.00
    other 0.84 0.73
    0.90 cTP 0.62 -
    mTP 0.76 0.65
    SP 0.00 0.00
    other 0.53 0.52

    The cutoffs above are based on TargetP performance on its redundancy-reduced test sets.

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.


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