plantiSMASH: Plant Secondary Metabolite Analysis

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Due to the limited server's resource, users can now only upload annotated fasta files (i.e. fasta + gff3). Please first run your assembly on gene finding tools such as AUGUSTUS or MAKER before submitting it into plantiSMASH. If you are analysing a publicly available genome, please check ‘Precalculated results’ first before submitting a job.

Search plant genome sequence for secondary metabolite biosynthesis gene clusters:

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:

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