LinksT6SS core components available at KEGG
T6SS descriptions available at MicrobeWiki
Bioinformatics tools used by SecReT6
- PostgreSQL, an open source relational database management system
- 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
Public database, to which SecReT6 has a hyperlink path
Other tools or servers of interest
- NCBI Microbial Genomes
- VFDB, Virulence Factor database
- Effective, a database of predicted secreted bacterial proteins
- 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
- 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
- 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.
- SCRATCH, a protein structure and structural feature prediction server.
- 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.