synthaser

synthaser parses batch NCBI conserved domain search results to annotate and classify megasynth(et)ase domain architectures in fungal polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs), linking secondary metabolites (SMs) to their biosynthetic origins.

Key Features:

• Batch Sequence Analysis: Processes batch NCBI conserved domain search results for large-scale analysis of multiple sequences.
• Hierarchical Rule-Based Classification System: Implements a customizable hierarchical rule-based classification for megasynth(et)ase domain architectures.
• Output and Visualization: Produces detailed textual outputs and visualizations representing domain architectures and annotations.
• NCBI CDD-based Domain Prediction: Uses NCBI Conserved Domain Database search results for domain prediction as an alternative to profile hidden Markov model (pHMM)-based approaches.

Scientific Applications:

• Large-Scale Genome Mining: Integrates into genome mining pipelines to identify and compare megasynth(et)ases across fungal genomes.
• PKS Similarity Network Construction: Supports construction of PKS similarity networks, exemplified by an Aspergillus PKS similarity network.
• Linking SMs to Biosynthetic Origins: Facilitates linking secondary metabolites (SMs) to biosynthetic genes and domain architectures in fungal genomes.

Methodology:

Uses batch NCBI Conserved Domain Database searches as input and applies a customizable hierarchical rule-based classification to predict and classify megasynth(et)ase domain architectures, distinguishing this approach from profile hidden Markov model (pHMM)-based methods.