MimicMe

By DoxeyLab . Find host-like proteins specific to pathogens.


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One way that pathogens exploit their hosts is by mimicking host proteins. MimicMe aims to predict host-like proteins (mimics) in pathogenic organisms. Mimics are identified as pathogen proteins that display a higher degree of sequence similarity to host proteins (targets) than that detected from control proteomes. MimicMe is best suited to identifying pathogen mimics that are homologous to a host protein. Mimicry of shorter motifs may be detectable through altered BLAST settings ("Short Motif Analysis") but this is still an experimental feature.

More details can be found in the original paper, which describes the analysis that was performed on Homo sapiens with a selection of 62 pathogens and 66 non-pathogens. An overview of the pipeline is shown below.
If you experience any problems with the tool, please contact acdoxey {at} uwaterloo {dot} ca.

How to MimicMe

  1. Select your analysis type. A homology analysis focuses on identifying mimicry of longer domains that have arisen through horizontal gene transfer or convergent evolution events, while a short motif analysis focuses on identifying mimicry of shorter motifs by using alternative BLAST settings.
  2. Select a host organism. Take note, once this step is complete, your session will be saved. Just bookmark this page in your browser and reload at a later time to work with the same set of host/pathogens/controls.
    You will also have the option of switching between organism type (eg. bacteria, viruses, fungi, or protozoa).
  3. Select your pathogen organisms.
  4. Select your control organisms.
  5. Tweak any additional enrichment-related settings.
  6. Submit and browse through all predicted mimics and host targets.

Start with one of the workflows here, and modify the input as necessary.

  • Homo sapiens
    • Broad analysis of human pathogens (Doxey & McConkey, 2013)
    • Mimicry in Legionella species
    • Mimicry in Francisella species
    • Mimicry in human viruses
    • Short motif mimicry in human viruses
  • Arabidopsis thaliana
    • Mimicry in Pseudomonas syringae.
  • Salmo salar
    • Mimicry in Flavobacterium pathogens.

How to Cite MimicMe

Petrenko P, Doxey AC. (2014) mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens. Bioinformatics, btu681. [pubmed]


Additional References

  • Doxey AC, McConkey BJ. (2013) Prediction of molecular mimicry candidates in human pathogenic bacteria. Virulence, 4:1-14. [pubmed]

Contact Us

Feel free to contact us anytime if you have any questions, concerns, or recommendations. In particular, please contact us if you would like to request additional host/microbial organisms for MimicMe.

Dr. Andrew C. Doxey: acdoxey

Pavel Petrenko (Developer): pavel.petrenko

Input
Predicted Mimicry Targets
Enriched Functions
Choose analysis type



Choose host

▶ Enrichment Settings

Integer >= 0
Integer > 0
Number > 0
Number >= 0
0 < eval ≤ .05
Pathogens

Please select host organism.
Controls

Please select host organism.


    ↑ To top of results

    Here you can launch an analysis to determine common or enriched functions among your list predicted host mimicry targets. If a particular gene ontology term is statistically enriched among your set of predictions compared to a background distribution for the entire host proteome, it will be listed here once the analysis is complete. The GO terms are also sorted using the fold enrichment of the go term as well as the number of representative predictions in which it appears.

    MSA & Conservation Among Pathogens

    yellow: residue is similar to host residue
    green: residue is identical to host residue
    The host residue uses the highest ranking color in the column.

    ×

    Structure & Conservation

    A host residue is conserved among pathogens if it is similar or identical to aligned residues in pathogen homologs:
    dark gray: unmapped, gray: not conserved, yellow: less conserved, green: more conserved

    Note, if you cannot see any molecule above, wait a few seconds. If nothing changes, please make sure you are using a newer version of Firefox, chrome, opera, safari, or IE. Otherwise, please use the other link to download the conservation colored PDB file and use a standalone program such as chimera to view the protein. ×

    A Problem Occurred



    Please contact acdoxey {at} uwaterloo {dot} ca if you need further assistance or if this problem keeps re-occuring.
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    Saved Session Loaded

    Your input has successfully been loaded from a previously saved session.

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    Suggested Organisms

    A list of pathogens/controls has been suggested for this particular host. Note that the suggestions are a small subset of all possible pathogen/control inputs for the current host organism. Feel free to use these suggestions or remove them using the clear buttons.

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