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Welcome to the fDOG wiki!
fDOG is a feature-aware directed ortholog search tool. For a single seed sequence, fDOG can find its orthologs and co-orthologs from different strains of the seed species or from distantly related taxa to draw the complete picture about the evolutionary history of the sequence of interest. fDOG is distributed as a python package called fdog. It is compatible with Python ≥ v3.9.
fDOG integrates the prediction of orthologs and the calculation of the Feature Architecture Similarty (FAS) scores. FAS scores are computed pairwise between the query gene and it's predicted orthologous genes using FAS tool, which will be automatically installed during the setup of fdog package. Combining both sequence similarity and feature architecture similarity, fDOG results are suitable for analysing not only the sequences themselves but also their functions throughout the evolution.
On the bases of fDOG the tool fDOG-Assembly was developed. While fDOG requires a protein set of every search species the tool fDOG-Assembly can search for orthologs in un-annotated genome assemblies. Candidate regions with high sequence similarity to the seed gene are determined with tBLASTn. Afterwards, a gene prediction step with the tools Augustus or MetaEuk result in candidate genes. The following orthology validation and FAS score computations are identical to the fDOG workflow.
In this wiki, you will find how to
- Install fDOG/ fDOG-Assembly and their dependencies
- Use the standalone version as well as the central installed version
- Add new taxa to fDOG
- Check the validity of your data for running fdog
- Merge outputs of several fdog run into one single output
Besides, we provide also a quick explanation of how fDOG works, a detailed information of the input and output files, some specific use-cases of fDOG and a FAQ section.
If this wiki cannot help you with your issue, please contact us! We are very happy to hear from your ;)