plantiSMASH: Plant Specialized Metabolite Analysis

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Developer notice

plantiSMASH 2.0 version is online, containing new and updated detection rules. Review the changes in our changelog here and on GitHub here.

To enable us to operate the plantiSMASH webserver with the resources available, users are expected to upload annotated Genbank-formatted or fasta files with gene/CDS annotations (i.e. fasta = gff3). Please first run your assembly on gene finding tools of your preference, such as AUGUSTUS or MAKER before submitting it into plantiSMASH. If you are analyzing a publicly available genome, please check the database of Precalculated Results first before submitting a job.

Search plant genome sequence for specialized metabolite biosynthesis gene clusters:

‼️ Before submitting a job, please check the plantiSMASH database of precalculated results to see if your genome of interest is already available.

For heavy jobs or to use some of the latest features (e.g., the TFBS Finder module), please consider running plantiSMASH locally via the command line. See the CLI documentation for details.

Email address (optional)

Load a file in GenBank / EMBL format (recommended) or in FASTA format

Annotation file in GFF3 format (mandatory!)

or input NCBI accession number of desired file

Additional analysis:

Gene cluster comparative analysis (ClusterBlast):

Compare to plantiSMASH predicted clusters

Compare to registered known clusters from MIBiG Database

Gene expression analysis (CoExpress):

Load a Gene Expression Omnibus (GEO) SOFT file or a properly formatted CSV file

Advanced options:

To further customize your analysis, consider running plantiSMASH locally via the command line.

Show advanced options

CD-HIT Cutoff

: (default: 0.5)

Minimum unique domains

: (default: 2)

MAD Cutoff (CoExpress)

: (default: not set; only filter out genes with 0 MAD)

Display results for an existing job