The output of the antiSMASH analysis pipeline is organized in an interactive HTML page with SVG graphics, and different parts of the analysis are displayed in different panels for every gene cluster (see example output file of Streptomyces coelicolor A3(2) genome).
Initially, a list of identified clusters is displayed in the results page. A gene cluster can be selected for viewing by clicking its number (gene clusters are numbered in the order in which they appear on the input nucleotide sequence) in the "Select Gene Cluster" panel just below the top banner or by clicking on the colored "Cluster XX" boxes. A click on "Overview" brings you back to the overview list. Gene cluster buttons are color coded by predicted secondary metabolite type.
In the upper panel, "Gene cluster description", information is given about each gene cluster that was detected. In the upper line, the biosynthetic type and location of the gene cluster are displayed. Underneath this title line, all genes present in a detected gene cluster are outlined. The borders of the gene clusters have been estimated using different greedily chosen cut-offs specified per gene cluster type. Genes are color coded by predicted function. Putative biosynthetic genes are colored red, transport-related genes are colored blue, and regulation-related genes are colored green. These predictions depend on the smCOG functionality an will be missing if you chose to not run smCOG predictions. Hovering over a gene with the mouse will prompt the gene name to be displayed above the gene. Clicking the gene will provide more information on the gene: its annotation, its smCOG (secondary metabolism gene family), its location, and cross-links specific to that gene.
In the middle panel, "Detailed annotation", you can find more in-depth information on the selected gene cluster. For predicted modular polyketide synthase (PKS) and/or nonribosomal peptide synthetase (NRPS) proteins, you will find the domain annotation. Clicking on a domain image will prompt more information to be displayed, such as the name of the detected domain, its precise location, any substrate specificites predicted, and a link to run Blast on the domain. For predicted Lantipeptide clusters, the predicted core peptide sequences of all identified prepeptides is displayed.
The lower panel. "Homologous gene clusters", displays the top ten gene clusters from the internal antiSMASH database that are most similar to a detected gene cluster, visually aligned to it. The drop-down selection menu can be used to browse through the gene clusters. Genes with the same colour are putative homologs based on significant Blast hits between them. In the upper side panel on the right. "Predicted core structure", a rough prediction of the overall chemical structure of a the product of a detected nonribosomal peptide or polyketide biosynthesis gene cluster is given, along with prediction details for all monomers. Prediction details are available for multiple methods.
PKS type I AT domain specificities are predicted using a twenty-four amino acid signature sequence of the active site (Yadav et al., 2003), as well as with pHMMs based on the method of Minowa et al. (Minowa et al., 2007), which is also used to predict co-enzyme A ligase domain specificities. NRPS A domain specificities are predicted using both the signature sequence method and the support-vector machines-based method of NRPSPredictor2 (Rausch et al., 2005 & Röttig et al., 2011), and the method of Minowa et al. (Minowa et al., 2007). Ketoreductase domain-based stereochemistry predictions for PKSs (Starcevic et al., 2008) are also performed.
For PKS type II clusters, the side panel shows a list of the predicted starter units along with bitscores, a list of the predicted number of malonyl elongations along with bitscores, the predicted product class, a list of product molecular weights predictions for each combination of starter unit and number of malonyl elongations. Furhtermore, it displays each gene/protein which are involved in the polyketide biosynthesis of the cluster. For each gene/protein the type is indicated and for some a prediction of function is displayed.
In the upper right, a small list of buttons offers further functionality. The house-shaped button will get you back on the antiSMASH start page. The question-mark button will get you to this help page. The exclamation-mark button leads to a page explaining about antiSMASH. The downward-pointing arrow will open a menu offering to download the complete set of results from the antiSMASH run, a summary Excel file and to the summary EMBL/GenBank output file. The EMBL/GenBank file can be viewed in a genome browser such as Artemis.