Gene-Cluster Discovery, Annotation and Visualization
Complete Gene Clusters by Adding Missing ORFs
Identify and Extract Gene Clusters from Scaled BLAST Data
Identify Breakpoints of Gene Clusters within a Contig
Plot Scaled Gene Clusters with Arrows
Extract ORF Positions for One Specific Gene Cluster
Determine ORF Range for a Candidate Gene Cluster
Scale Gene-Cluster Coordinates for Visualization
Gene-Cluster Discovery, Annotation and Visualization
Remove Length Outliers from BLAST Results
Extract ORF and Genome Information from BLAST or BLASTP Results
Parse ORF Coordinates from Prodigal FASTA Headers
Performs end-to-end analysis of gene clusters—such as photosynthesis, carbon/nitrogen/sulfur cycling, carotenoid, antibiotic, or viral marker genes (e.g., capsid, polymerase, integrase)—from genomes and metagenomes. It parses Basic Local Alignment Search Tool (BLAST) results in tab-delimited format produced by tools like NCBI BLAST+ and Diamond BLASTp, filters Open Reading Frames (ORFs) by length, detects contiguous clusters of reference genes, optionally extracts genomic coordinates, merges functional annotations, and generates publication-ready arrow plots. The package works seamlessly with or without the coding sequences input and skips plotting when no functional groups are found. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.