workbench MCP Tools
workbench exposes 144 tools. Each one has its own page with the configuration for every client that can run this server.
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reverse_complementreverse complement
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gc_contentgc content
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translatetranslate
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find_orfsRead-onlyfind orfs
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format_sequenceformat sequence
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motif_findermotif finder
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reverse_translatereverse translate
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random_sequencerandom sequence
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melting_temperaturemelting temperature
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annealing_temperatureannealing temperature
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oligo_analysisoligo analysis
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in_silico_pcrin silico pcr
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primer_designprimer design
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dna_molaritydna molarity
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site_directed_mutagenesissite directed mutagenesis
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oligo_pool_screenoligo pool screen
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cross_dimercross dimer
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primer_specificityprimer specificity
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oligo_cofoldoligo cofold
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barcode_designbarcode design
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barcode_auditbarcode audit
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restriction_sitesrestriction sites
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double_digestdouble digest
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cloning_simulatecloning simulate
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plasmid_annotateplasmid annotate
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construct_qcconstruct qc
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construct_autofixconstruct autofix
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virtual_gelvirtual gel
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ligation_setupligation setup
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gel_band_sizegel band size
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golden_gate_from_partsgolden gate from parts
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assembly_outcomesassembly outcomes
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diagnostic_digestdiagnostic digest
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repeat_instabilityrepeat instability
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nonrepetitive_parts_findnonrepetitive parts find
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nonrepetitive_parts_designnonrepetitive parts design
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operon_scanoperon scan
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operon_designoperon design
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synthesis_complexitysynthesis complexity
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band_tracebackband traceback
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sanger_indel_spectrumsanger indel spectrum
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outcome_deconvolveoutcome deconvolve
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trace_secondary_peakstrace secondary peaks
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trace_diagnosetrace diagnose
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primer_site_accessibilityprimer site accessibility
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promoter_predictpromoter predict
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promoter_library_designpromoter library design
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cloning_next_observationcloning next observation
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read_placement_planRead-onlyread placement plan
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base_edit_quantbase edit quant
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sanger_knockin_quantsanger knockin quant
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editing_plate_quantifyediting plate quantify
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multiplex_panel_designmultiplex panel design
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cloning_diagnosecloning diagnose
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protein_propertiesprotein properties
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protein_hydrophobicityprotein hydrophobicity
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protease_digestionprotease digestion
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codon_optimizecodon optimize
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codon_adaptation_indexcodon adaptation index
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pairwise_alignmentpairwise alignment
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multiple_sequence_alignmentmultiple sequence alignment
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variant_comparatorvariant comparator
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dot_plotdot plot
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identity_matrixidentity matrix
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sanger_plate_verifysanger plate verify
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crispr_grna_designcrispr grna design
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crispr_offtarget_checkcrispr offtarget check
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crispr_hdr_donorcrispr hdr donor
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crispr_ontargetcrispr ontarget
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elsa_capacityelsa capacity
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elsa_designelsa design
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parse_genbankparse genbank
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sequence_format_convertsequence format convert
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seqfile_statsseqfile stats
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parse_sanger_traceparse sanger trace
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sanger_vs_referencesanger vs reference
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parse_snapgeneparse snapgene
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sanger_assemblesanger assemble
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characterize_sequencecharacterize sequence
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sequence_reportsequence report
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cpg_islandscpg islands
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parse_gff3parse gff3
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blast_submitblast submit
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blast_pollblast poll
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od600_cellsod600 cells
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qpcr_ddctqpcr ddct
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centrifuge_conversioncentrifuge conversion
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solution_prepsolution prep
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session_createsession create
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session_getsession get
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session_setsession set
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session_runsession run
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sequence_fetchsequence fetch
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sequence_searchsequence search
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protein_annotate_submitprotein annotate submit
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protein_annotate_pollprotein annotate poll
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plasmid_identifyplasmid identify
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plasmid_full_reportplasmid full report
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plasmid_dossierplasmid dossier
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plasmid_deep_annotateplasmid deep annotate
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verify_constructverify construct
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verify_assemblyverify assembly
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golden_gate_fidelitygolden gate fidelity
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golden_gate_designgolden gate design
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save_permalinksave permalink
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sequencing_readback_verifysequencing readback verify
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whole_plasmid_verifywhole plasmid verify
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web_searchweb search
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id_map_submitid map submit
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id_map_pollid map poll
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ortholog_maportholog map
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volcano_plot_datavolcano plot data
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expression_heatmap_clusterexpression heatmap cluster
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functional_enrichmentfunctional enrichment
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hgvs_converthgvs convert
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fastq_qc_reportfastq qc report
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fastq_trimfastq trim
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alphafold_lookupalphafold lookup
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export_plate_layoutRead-onlyexport plate layout
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export_opentrons_protocolRead-onlyexport opentrons protocol
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export_echo_picklistRead-onlyexport echo picklist
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variant_annotatevariant annotate
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variant_to_constructvariant to construct
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gene_modelgene model
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gene_dossiergene dossier
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gene_expressiongene expression
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prime_editing_designprime editing design
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prime_editing_twin_designprime editing twin design
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prime_editing_efficiencyprime editing efficiency
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base_editing_designbase editing design
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sirna_designsirna design
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aso_designaso design
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kasp_primer_designkasp primer design
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rna_foldrna fold
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rbs_predictrbs predict
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rbs_designrbs design
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rbs_library_designrbs library design
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rbs_occlusionrbs occlusion
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riboswitch_statesriboswitch states
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vector_library_searchvector library search
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vector_library_getvector library get
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parts_library_searchparts library search
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batchbatch
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workflowworkflow
This list was read from the server itself, by connecting to it and calling tools/list on 24 September 2026. It is what
the server actually exposes, not what its listing claims.
Mutating and Read-only are read off each tool's name, not its schema — a hint, not a guarantee. The registry stores tool names only; connect the server for its live schemas.