Archive of effectors.org

For all effectors.org versions starting from 3.0 (12/2012) we have archived the database tables
of eukaryotic-like domains and the pre-calculated annotations of bacterial genomes. For older
versions, unfortunately, archive data are incomplete (only pre-calculated genomes for 1.0) or
missing (2.0).



Eukaryotic-like domains:
Three tables store the eukaryotic-like domains in the effectors.org database. These are dumped as tab-delimited files.

euk_domain.txt (Non-pathogenic frequencies of eukaryotic-like domains in genomes of non-pathogens)
Column 1:	domainid (protein domain ID)
Column 2:	description (protain domain description)
Column 3:	nonpath_avg_simap (average occurrence of domain in non-pathogens in original RefSeq/Genbank genome annotation, taken from SIMAP database)
Column 4:	nonpath_stddev_simap (standard deviation of the occurrence of domain in non-pathogens in original RefSeq/Genbank genome annotation, taken from SIMAP database)
Column 5:	nonpath_avg_eggnog (average occurrence of domain in the conserved fraction of genome, taken from eggNOG database)
Column 6:	nonpath_stddev_eggnog (standard deviation of the occurrence of domain in the conserved fraction of genome, taken from eggNOG database)

euk_prediction.txt (Annotation of proteins with eukaryotic-like domains)
Column 1:	gpid (genome project ID)
Column 2:	accession (protein accession)
Column 3:	domainid (protein domain ID)

euk_score.txt (Genome-specific scores of eukaryotic-like domains)
Column 1:	domainid (protein domain ID)
Column 2:	gpid (genome project ID)
Column 3:	score_simap (genome-specific Z-score, based on the original RefSeq/Genbank genome annotation, taken from SIMAP database)
Column 4:	score_eggnog (genome-specific Z-score, based on the conserved fraction of genome, taken from eggNOG database)

Additionally, the genome table stores the genome repository:
Column 1:	gpid (genome project ID)
Column 2:	taxonomyid (NCBI taxonomyid)
Column 3:	refseq_accessions (NCBI RefSeq accessions)
Column 4:	genbank_accessions (NCBI GenBank accessions)
Column 5:	description (genome description)
Column 6:	class (type of genome: pathogen, symbiont or non-pathogen)
Column 7:	gramstatus (gram status)
Column 8:	hasT3 (encodes complete T3 secretion system)
Column 9:	strain (so far not used)


Pre-calculated genome annotations:
All files are stored in their original format in the genomes.zip archive.