zDB documentation¶
Note
Problems and errors encountered on the zDB website can be announced on the github page of the website
Contents:
- Methods
- Overview
- NextFlow pipeline
- Selection of PVC genomes integrated into the database
- Protein annotation
- Homology search (RefSeq and SwissProt)
- Identification of Orthogroups
- Orthogroup multiple sequence alignments & phylogenies
- Phlogeny including top RefSeq hits
- Calculation of pairwise protein identity
- Circular genome plots (Circos)
- Species phylogeny
- Prediction of protein-protein interactions
- Prediction of candidate type III secretion system effectors
- Taxonomic profile of Pfam domains and COGs
- Evaluation of the quality and completeness of draft genomes
- Pubmed References
- Protein accessions mapping
- SQL database and Web Interface
- Source databases
- Software versions
- Code availability
- Website tutorial