TargetP - 2.0
Subcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other
TargetP-2.0 server predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (lTP). For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.
1. Specify the input sequencesAll the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:
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
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.
2. Customize your run
- Organism group:
Choose Plant for any organism with chloroplasts/plastids and Non-plant otherwise.
- Output format:
You can choose between two output formats:
- Shows one plot and one summary per sequence.
- Convenient if you submit lots of sequences. Shows only one line of output per sequence and no graphics.
3. Submit the jobClick 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 OutputsTo appear...
Training and testing data set
The dataset used for training, validating, and testing TargetP 2.0 (using nested cross-validation) can be found here.
The sequences are in FASTA format with the UniProt AC as sequence name: Download
The annotations are in a tab-separated file where each line contains three fields: The UniProt AC, the type of targeting peptide,
and the length of the targeting peptide.
The type can be
- "SP" for signal peptide,
- "MT" for mitochondrial transit peptide (mTP),
- "CH" for chloroplast transit peptide (cTP),
- "TH" for thylakoidal lumen composite transit peptide (lTP),
- "Other" for no targeting peptide (in this case, the length is given as 0).
Predictions on proteomesResults from TargetP predictions on whole proteomes from UniProt (gzipped text files):
José Juan Almagro Armenteros, Marco Salvatore, Ole Winther, Olof Emanuelsson, Gunnar von Heijne, Arne Elofsson, and Henrik Nielsen
Life Science Alliance 2 (5), e201900429. doi:10.26508/lsa.201900429 (Open access)
The current server. New in this version: