The virulence factor/regions of interest databases used in the ST131 project.
- MANIFEST:
- ALL_FEATURES.fa (concatenation of all unique features)
- Antibiotics.fa (bla-CTX-M-1 for CTX-15)
- Antibiotics_CTX-15.fa
- Autotransporters.fa (42). Based on Wells et al. (FIXED)
- Colicins_and_microcins.fa (21)
- CU_fimbriae.fa (38). Based on Wurpel et al. (FIXED)
- fimB.fa (wt and IS)
- Iron_uptake.fa (15) (FIXED)
- Islands.fa (not if SeqFindR format, use chunk_mfa.py)
- Islands_500bp_chunks.fa
- O_antigen.fa (from Islands.fa)
- Other_virulence_genes.fa (30)
- plasmid_replicons.fa
- Schembri_VFDB.fa (Autotransporters, Colicins_and_microcins, CU_fimbriae, Iron_uptake, Other_virulence_genes, Toxins, UPEC_specific_genes)
- Toxins.fa (4) (FIXED)
- UPEC_specific_genes.fa (125). Based on Mobley et al. (FIXED)
- The following were duplicates across the pooled database:
- c0393
- c4308
- c3610
- c3619
- c2436
- c1374
- c2482
- c2775
On the 07/06/2013 Mat Upton pointed out that there was an issues with some sequences in the database. This was due to a bug in the KEGG extract script.
- The following databases are not effected:
- Antibiotics.fa & Antibiotics_CTX-15.fa
- Colicins_and_microcins.fa
- fimB.fa
- Islands.fa
- Islands_500bp_chunks.fa
- Other_virulence_genes.fa
- O_antigen.fa
- plasmid_replicons.fa
- Suggested labels:
- CU fimbriae
- Autotransporters
- Toxins
- Iron uptake
- Colicins and microcins
- Other virulence genes
- UPEC specific genes