Metamenu

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Tutorials

Frequently asked questions (FAQ)

Q: Why the results with different arguments varies considerably, especially when I add EffectiveS346 arguments?

A: You've actually observed one difference in your prediction, which is the difference in predicted effectors by EffectiveELD. This difference is intended. In protein mode, the server does not consider your proteins a complete genome. It can therefore not obtain counts of domain frequencies directly from your data. Therefore eukaryotic-like domains, which have been observed significantly enriched in any of the pathogen/symbiont genomes from the Effective genome repository, are reported. These are many. In genome mode, domain frequency counts are directly obtained from your data. This gives much less, but much more specific results. Effective then only reports ELD which are significantly enriched in _YOUR_ genome. That makes the difference.

Q: Can I run all these tools you used for the database also locally on new sequences/genomes?

A: Yes, our computer cluster would be pleased! But we are aware that this needs some effort in installing. For instructions and documentation see 'Methods' and 'downloads' on this page.

Q: What does this 'N.D.' mean, which I see sometimes at 'Gram negative:' and following lines?

A: This means 'not defined', which is the case for genome based results when not the full data of a genome is provided or when the genome mode is disabled.

Q: Which publication should I cite when I am using results from the database and/or website?

A: You should cite at least the latest Effective/EffectiveDB paper. As the database and website is collecting results also from other tools, you should cite these as well, especially when relying on these results. Please see for this 'Methods' and 'Publications' on this page.