| Bioinformatics tools used by VRprofile |
- PostgreSQL, an open source relational database management system
- MultiGeneBlast, an open source tool for identification of homologs of multigene modules.
- HMMER, Biosequence analysis using profile hidden Markov models
- WU-BLAST, the Washington University improved version of BLAST
- MUSCLE, protein multiple sequence alignment
- Jalview, a multiple alignment editor written in Java
- CGview, generate circular genome maps
- MUMmer, genome alignment and scaffold reorder
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| Public database, to which VRprofile has a hyperlink path |
- NCBI
- NCBI COG
- Uniprot KB
- STRING
- NCBI CDD
- Sanger Pfam
- T3DB, an integrated database for bacterial Type III Secretion System and cognate effectors
- T3SEdb, data warehousing of virulence effectors secreted by the bacterial Type III Secretion System
- CONJscan, Search for relaxases and key components of type IV secretion systems in proteomes using an HMM profiles database
- AtlasT4SS, a curated database for type IV secretion systems
- CONJdb, allows searching and browsing Conjugative Type IV Secretion and Mobilization Systems via a graphical interface
- SecReT4, a database for gene clusters encoding type IV secretion system
- SecReT6, a web-based resource for bacterial type VI secretion system
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| Other tools or servers of interest |
- NCBI Microbial Genomes
- VFDB, Virulence Factor database
- ARDB, Antibiotic Resistance Genes Database
- CARD, The Comprehensive Antibiotic Resistance Database
- ACLAME, A Classification of Genetic Mobile Elements
- DEG, Database of essential genes
- DrugBank, a knowledgebase for drugs, drug actions and drug targets
- TTD, Therapeutic Target Database
- BacMet, Antibacterial biocide and metal resistance genes database
- PhyML, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies
- iTOL, Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees
- T3DB, an integrated database for bacterial Type III Secretion System and cognate effectors
- T3SEdb, data warehousing of virulence effectors secreted by the bacterial Type III Secretion System
- AtlasT4SS, a curated database for type IV secretion systems
- SecReT4, a database for gene clusters encoding type IV secretion system
- MultiGeneBlast, an open source tool for identification of homologs of multigene modules such as operons and gene clusters. It is based on a reformatting of the FASTA headers of NCBI GenBank protein entries, using which it can track down their source nucleotide and coordinates.
- SSPred, a prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems.
- PHAST(PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.
- GOLD, Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.
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