Eff3ctidor

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Select an input ORFs file:

Select an input effectors file (optional):

Do you want us to add putative effectors to your effectors data, that will be used together with your data as positive samples, based on homology to our effectors dataset? Yes No

E-mail:

Job title:

Would you like to include a prediction of the secretion signal in your analysis?
Yes No

Upload effectors file for homology search:

Upload a host proteome archive:

Upload an archive with proteome records of closely related bacteria without T3SS:

Upload a GFF3 file:

To search for regulatory motifs in the promoters of the genes please supply the following data:

Upload a full genome FASTA file:

Select regulatory elements to be searched for in the promoters:

PIP-box
hrp-box
mxiE-box
exs-box
tts-box

Input specification

The input for Effectidor is a text file with all the Open Reading Frames (ORFs) sequences of the analyzed genome. The file should be in a DNA FASTA format.
You can find instructions to download this file here.
If the analyzed genome is composed of a chromosome and plasmids, the ORFs from each can be supplied in separate files. In this case, the files should be compressed together in a ZIP archive.
Please make sure all the files packed in your input zip archive are in DNA FASTA format, and are not packed in directories - Directories within the zip archive are ignored.

Note, only protein coding genes should be included in this input. Non-coding RNA genes, such as tRNA, should not be included. If you follow the instructions above, no such genes are expected in your input file. Alternatively, if such RNA genes do appear in your data and you supply a GFF3 file indicating it (in the advanced options), we will filter them out automatically.

Input specification

This file should be in a DNA FASTA format. The records supplied in this file must be copied from the main ORFs file, and will be treated as "known effectors" to train the machine-learning algorithm.
This is an optional (and recommended) input. If you choose not to supply it, the records that show high sequence similarity to our effectors dataset (see "Data") will be used as the "known effectors".
Please note that the predictions are conducted after training the machine-learning algorithm on these "known effectors" of the given genome, and no exterior effectors data are used for training. Thus, it is most recommended to add these records to achieve better predictions of potential novel T3Es. This is especially important when not many effectors are known in the bacterial genome you are analyzing.

Input specification

In this input you may upload a protein FASTA file with type 3 effector records of other bacteria to be used in addition to our effectors dataset for homology searches.

Input specification

In this input you may upload host proteome(s).
You should upload protein FASTA file(s), compressed together in a zip archive.
The files should not be packed inside directories - directories packed in the zip archive will be ignored. Also files with names starting with a dot (.) or an underscore (_) will be ignored.

If you upload this archive, a BLAST will be run against all the protein sequences in the compressed FASTA files. Sequence similarity of the bacterial proteins to host proteins is potentially a very important feature for the classification as it captures Eukaryotic domains within the bacterial proteins.

Input specification

In this input you may upload proteome(s) of closely related bacteria that do not encode a T3SS.
You should upload protein FASTA files, such that each FASTA file contains all the protein sequences of a single bacterium, compressed together in a zip archive.
The files should not be packed inside directories - directories packed in the zip archive will be ignored. Also files with names starting with a dot (.) or an underscore (_) will be ignored.

These data will be used for sequence similarity search. Each FASTA file within the zip archive will be used for a different search. Sequence similarity to proteins of closely related bacteria without a T3SS is a strong negative feature for T3Es classification.

Input specification

GFF3 files will be used for extraction of genome organization features.
If you wish to upload more than one file (for example, if a plasmid is available), compress them in a single zip archive.
The files should not be packed inside directories - directories packed in the zip archive will be ignored. Also files with names starting with a dot (.) or an underscore (_) will be ignored.

Input specification

These files will be used to search for cis-regulatory elements in the promoters of the genes, according to your selection.
The regulatory elements available for search are PIP-box, hrp-box, mxiE-box, exs-box, and tts-box.

If you wish to upload more than one file (for example, if a plasmid is available), compress them in a single zip archive.
The files should not be packed inside directories - directories packed in the zip archive will be ignored. Also files with names starting with a dot (.) or an underscore (_) will be ignored.

Input specification

The previous effectors input is optional, and if not supplied we build the effectors set based on homology to an established effectors dataset. Since you supplied an effectors data, we can either use it as the only positive set, or we can add to it ORFs from your input that share high homology to our effectors dataset. Choose "yes" if you want us to search for additional effectors based on homology to use us for the training, and "no" if you want your input to be the only one used in the positive set.

Please note that homology to our effectors data is used as a feature in any case.

Input specification

PIP-box is relevant for Xanthomonas, Ralstonia, and Acidovorax.
hrp-box is relevant for Pseudomonas syringae and plant pathogens of the family of Enterobacteria.
mxiE-box is relevant for Shigella.
exs-box is relevant for Pseudomonas aeruginosa.
tts-box is relevant for rhizobia.

Make sure to choose only regulatory elements that are relevant for the bacterium you analyze. Non-relevant regulatory elements may hamper the classification accuracy.

Input specification

For explanation regarding our use of your E-mail: see FAQ

Input specification

This feature can help us find potential T3Es. The disadvantage of this inclusion: longer running time of Effectidor.
More information is available in this paper. Please refer to this paper if you use this feature in your analysis.