bolognabiocomp/tppred3 repository overview

⁠tppred3 - Organelle-targeting peptide prediction

⁠Publication

Savojardo C., Martelli P.L., Fariselli P., Casadio R. TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in Eukaryotic proteins⁠, Bioinformatics (2015) 31(20): 3269-3275.

⁠The TPpred3 Docker image

Image availbale on DockerHub https://hub.docker.com/r/bolognabiocomp/tppred3⁠

⁠Usage of the image

The first step to run TPpred3 Docker container is the pull the container image. To do so, run:

$ docker pull bolognabiocomp/tppred3

Now the TPpred3 Docker image is installed in your local Docker environment and ready to be used. To show TPpred3 help page run:

$ docker run bolognabiocomp/tppred3 -h

usage: tppred3.py -f FASTA_File [-k P,N] [-o out_file]

 tppred3.py: Prediction of organelle targeting peptides in proteins.

   Copyright (C) 2015 Castrense Savojardo
   Bologna Biocomputing Group
   University of Bologna, Italy.
   [email protected]

optional arguments:
  -h, --help  show this help message and exit

OPTIONS:
  -f FILE     Protein sequences in FASTA format. Required.
  -o FILE     Output prediction file. Optional, default: STDOUT.
  -k {P,N}    Protein kingdom: P="Plant" or N="non-Plant"

The program accepts three arguments:

• The full path of the input FASTA file containing protein sequences to be predicted;
• The output file where predictions will be stored;
• The kingdom the sequences belong to. You must specify "P" for plant species or "N" for non-plant species. When plant (P) is specified, TPpred3 predicts also chloroplastic targeting signals whereas only mitochondrial signals are predicted for non-plant sequences. The defualt value is plant mode (P).

Let's now try a concrete example. First of all, let's downlaod an example sequence from UniProtKB, e.g. the human Enoyl-CoA hydratase, mitochondrial (accession P30084):

$ wget http://www.uniprot.org/uniprot/P30084.fasta

Now, we are ready to predict the targeting peptide of our input protein. Run:

$ docker run -v $(pwd):/data/ bolognabiocomp/tppred3 -f P30084.fasta -o P30084.gff -k N

In the example above, we are mapping the current program working directory ($(pwd)) to the /data/ folder inside the container. This will allow the container to see the external FASTA file P30084.fasta. The file P30084.gff now contains the TPpred3 prediction in GFF3 format:

$ cat P30084.gff

sp|P30084|ECHM_HUMAN	TPpred3	Transit peptide	1	27	0.61	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P30084|ECHM_HUMAN	TPpred3	Chain	28	290	.	.	.	evidence=ECO:0000256
sp|P30084|ECHM_HUMAN	fimo	Motif	25	28	9.52	.	.	Name:Mitochondrion cleavage-site motif 1 (RC|[YF][AS]);matching_sequence=RPFA;evidence=ECO:0000256;Dbxref=PMID:26079349

Columns are as follows:

• Column 1: the protein ID/accession as reported in the FASTA input file;
• Column 2: the name of tool performing the annotation (either TPpred3 or fimo for Motifs, see below)
• Column 3: the annotated feature alogn the sequence. Can be "Transit peptide", "Chain" (indicating the mature protein) or "Motif" (for reporting cleavage-site motif occurrence)
• Column 4: start position of the feature;
• Column 5: end position of the feature;
• Column 6: feature annotation score (as assigned by TPpred3 for transit peptides or fimo for motifs);
• Columns 7,8: always empty, reported for compliance with GFF3 format
• Column 9: Description field. In Note, the type of transit pepetide is reported (either Mitochondrion or Chloroplast). Gene Ontology Cellular Component terms are also reported (only when a transit peptide is detected). For Chain features, only evidence code is reported. In case of Motifs, the description reports the motif name, the motif degenerate sequence and the actual sequence match. For more details about cleavage-site motifs, please see the TPpred3 publication⁠.

⁠Install and use TPpred3 from source

Source code available on GitHub at https://github.com/BolognaBiocomp/tppred3⁠.

⁠Installation and configuration

TPpred3 is designed to run on Unix/Linux platforms. The software was written using the Python programming language and it was tested under the Python version 3.

To obtain TPpred3, clone the repository from GitHub:

$ git clone https://github.com/BolognaBiocomp/tppred3

This will produce a directory “tppred3”. Before running tppred3 you need to set and export a variable named TPPRED_ROOT to point to the tppred3 installation dir:

$ export TPPRED_ROOT='/path/to/tppred3'

Before running the program, you need to install TPpred3 dependencies. We suggest to use Conda (we suggest Miniconda3⁠) create a Python virtual environment and activate it.

To create a conda env for tppred3:

$ conda create -n tppred3

To activate the environment:

$ conda activate tppred3

The following Python libraries/tools are required:

• biopython
• emboss
• meme
• libsvm

To install all requirements run the followgin commands:

$ conda install meme emboss -c bioconda
$ conda install libsvm -c conda-forge
$ conda install libiconv biopython

Now you are able to use tppred3 (see next Section). Remember to keep the environment active. If you whish, you can copy the “tppred3.py” script to a directory in the users' PATH.

⁠Usage

The program accepts three arguments:

• The full path of the input FASTA file containing protein sequences to be predicted;
• The output file where predictions will be stored;
• The kingdom the sequences belong to. You must specify "P" for plant species or "N" for non-plant species. When plant (P) is specified, TPpred3 predicts also chloroplastic targeting signals whereas only mitochondrial signals are predicted for non-plant sequences. The defualt value is plant mode (P).

As an example, run the program on the example FASTA file contained in the folder "example":

$ ./tppred3.py -f example/example.fasta -k P -o example/example.out

This will run tppred3 on sequences contained in the "example/example.fasta" file, in plant mode and storing the output in the "example/example.out" file.

Once the prediction is done, the GFF3 output should look like the following (columns are as described above):

$ cat example/example.out

##gff-version 3
sp|P30084|ECHM_HUMAN	TPpred3	Transit peptide	1	27	0.61	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P30084|ECHM_HUMAN	TPpred3	Chain	28	290	.	.	.	evidence=ECO:0000256
sp|P30084|ECHM_HUMAN	fimo	Motif	25	28	9.52	.	.	Name:Mitochondrion cleavage-site motif 1 (RC|[YF][AS]);matching_sequence=RPFA;evidence=ECO:0000256;Dbxref=PMID:26079349
sp|P36957|ODO2_HUMAN	TPpred3	Transit peptide	1	67	0.91	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P36957|ODO2_HUMAN	TPpred3	Chain	68	453	.	.	.	evidence=ECO:0000256
sp|Q86U06|RBM23_HUMAN	TPpred3	Chain	1	439	1.0	.	.	evidence=ECO:0000256
sp|P38646|GRP75_HUMAN	TPpred3	Transit peptide	1	46	0.83	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P38646|GRP75_HUMAN	TPpred3	Chain	47	679	.	.	.	evidence=ECO:0000256
sp|P38646|GRP75_HUMAN	fimo	Motif	44	47	9.6	.	.	Name:Mitochondrion cleavage-site motif 1 (RC|[YF][AS]);matching_sequence=RDYA;evidence=ECO:0000256;Dbxref=PMID:26079349
sp|P48047|ATPO_HUMAN	TPpred3	Transit peptide	1	23	0.84	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P48047|ATPO_HUMAN	TPpred3	Chain	24	213	.	.	.	evidence=ECO:0000256
sp|P48047|ATPO_HUMAN	fimo	Motif	22	25	9.52	.	.	Name:Mitochondrion cleavage-site motif 1 (RC|[YF][AS]);matching_sequence=RPFA;evidence=ECO:0000256;Dbxref=PMID:26079349
sp|P48201|AT5G3_HUMAN	TPpred3	Transit peptide	1	67	0.73	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P48201|AT5G3_HUMAN	TPpred3	Chain	68	142	.	.	.	evidence=ECO:0000256
sp|P49411|EFTU_HUMAN	TPpred3	Chain	1	452	0.72	.	.	evidence=ECO:0000256
sp|P49448|DHE4_HUMAN	TPpred3	Transit peptide	1	53	0.81	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P49448|DHE4_HUMAN	TPpred3	Chain	54	558	.	.	.	evidence=ECO:0000256
sp|P49448|DHE4_HUMAN	fimo	Motif	51	54	11.03	.	.	Name:Mitochondrion cleavage-site motif 1 (RC|[YF][AS]);matching_sequence=RHYS;evidence=ECO:0000256;Dbxref=PMID:26079349
sp|P55084|ECHB_HUMAN	TPpred3	Transit peptide	1	34	0.72	.	.	Note:Mitochondrion;Ontology_term:GO:0005739;evidence=ECO:0000256
sp|P55084|ECHB_HUMAN	TPpred3	Chain	35	474	.	.	.	evidence=ECO:0000256
sp|P55084|ECHB_HUMAN	fimo	Motif	31	38	0.09	.	.	Name:Mitochondrion cleavage-site motif 2 (SVRx|Y[SA][TS]G);matching_sequence=QLRAAPAV;evidence=ECO:0000256;Dbxref=PMID:26079349

Please, reports bugs to: [email protected]⁠