Jean by Melad Labs
The bioinformatics & biotech suite, callable by any AI assistant
279 scientific tools · one URL · no key · free
Design the construct · Simulate the bench step · Analyze what comes back · Verify the result
Connect · How it works · What to ask · Every tool · FAQ
Your assistant is brilliant at reasoning and unreliable at science it has to compute.Ask it for a melting temperature, a Gibson overlap, a ΔΔCq, a phylogeny or a peptide mass, and itanswers from memory: fluently, confidently, and sometimes wrong. A wrong primer costs a week.A wrong conclusion costs a paper.
Jean is a bioinformatics and biotech suite (scientific computing for the life sciences), and this is its door for AI.One engine, validated against the reference implementations of each field, served over theModel Context Protocol. Connect it once, and Claude, ChatGPT, Cursor,VS Code or any MCP client can compute the answer instead of guessing it, across the whole arc of anexperiment:
| 🧬 Design | Constructs and assemblies, every primer and oligo, CRISPR guides, codon-optimized genes, RBS sites and operons, in-situ probes, barcodes, genetic circuits, variant libraries |
| 🧪 Simulate | Digests and gels, PCR products, multiplex screens, Gibson, Golden Gate and Gateway reactions, run on paper before they are run at the bench |
| 📊 Analyze | Sanger traces and NGS reads, qPCR and ddPCR runs, variants and copy number, expression and enrichment, phylogenies, mass-spec proteomics, antibodies, structures and small molecules |
| ✅ Verify | Prove the clone you got is the construct you drew, screen for vector contamination, recover how a construct was made |
🎯 Calculated, not recalledThermodynamics, enzyme specificity, alignment scores and statistics are computed on every call, byengines checked against the reference tools the field already relies on. |
🔍 Explained, not assertedEach answer carries its derivation: the method, the parameters, the inputs, and what would undermineit. A reviewer can reproduce every number. |
🔒 Private, not storedThe server is stateless: nothing you send is kept or carried between calls. No account, no key, notracking. |
⚡ Connect in thirty seconds
| Setting | Value |
|---|---|
| Server URL | https://jeanslabs.vercel.app/mcp |
| Transport | Streamable HTTP |
| Authentication | None |
| Cost | Free |
Claude (claude.ai, Desktop): ➕ Add Jean as a connector. The dialog opens prefilled.
Claude Code:
claude mcp add --transport http jean https://jeanslabs.vercel.app/mcp
Cursor, in ~/.cursor/mcp.json:
{ "mcpServers": { "jean": { "url": "https://jeanslabs.vercel.app/mcp" } } }
VS Code, in .vscode/mcp.json:
{ "servers": { "jean": { "type": "http", "url": "https://jeanslabs.vercel.app/mcp" } } }
Any other MCP client: add a remote server with the URL above. Field-by-field help for everyconnector dialog is at jeanslabs.vercel.app/docs/api/mcp.
🔁 How it works
sequenceDiagram
participant You
participant Assistant as Your AI assistant
participant Jean
participant DB as Public databases (NCBI, EMBL-EBI, UCSC, UniProt)
You->>Assistant: Clone GFP into pET-28a with NdeI and XhoI
Assistant->>Jean: fetch the vector record
Jean->>DB: query by accession
DB-->>Jean: GenBank record
Assistant->>Jean: design primers, simulate PCR and digest
Jean-->>Assistant: primers, Tm values, product map, method and parameters
Assistant-->>You: a plan you can check, number by number
The assistant decides what to do; every number comes from Jean. Results are structured data thatmatch a declared schema, and anything visual (a plasmid map, a gel, a trace, a tree, a plot) comesback as both SVG and PNG. Workflow tools chain steps into a reproducible pipeline that runs in one call.
💬 What you can ask
| Field | Try asking |
|---|---|
| Cloning | "Put GFP into pET-28a between NdeI and XhoI. Design the primers, check both enzymes cut the vector once, and show me the final map." |
| Assembly | "Plan a four-part Gibson assembly of these fragments and give me the overlaps and their Tm." · "Will these Golden Gate overhangs ligate faithfully?" |
| Sequencing | "Here are three Sanger reads of my clone. Is the insert correct, base for base?" |
| Genome editing | "Design guides against exon 2 of this gene and rank them by predicted efficiency and off-target risk." · "Quantify the indels in this edited trace against the control." |
| qPCR & dPCR | "Fit these amplification curves and give me ΔΔCq against GAPDH, with uncertainty." |
| Genomics | "Read this VCF and give me allele frequencies and Fst per population." · "Run gene-set enrichment on my differentially expressed genes." |
| Proteins | "Which proteins do these peptide-spectrum matches support?" · "Number this antibody, type the chain, and list its sequence liabilities." |
| Chemistry | "Cluster these compounds, show me the scaffolds, and flag activity cliffs." |
| Evolution | "Align these sequences, pick the best substitution model, build a maximum-likelihood tree with support, and draw it." |
A thirty-second honesty test. Ask for EcoRI sites on the circular sequence
AATTCTTAGGATCCG.The only site spans the point where the circle closes, so an answer that treats the sequence as astraight line finds nothing. Jean finds it. Ask for an enzyme that does not exist, and Jean says soby name instead of returning an empty list that reads as "no sites".
👩🔬 Built for
| You are | Jean gives your assistant |
|---|---|
| A wet-lab biologist | Primers, digests, assemblies and verification you can order from with confidence |
| A synthetic biologist | Golden Gate and MoClo grammars, overhang fidelity, RBS and operon design, genetic circuits |
| A core facility | Trace QC, construct verification, and qPCR and ddPCR analysis that explains itself |
| A computational biologist | Alignment, phylogenetics, variants, copy number, expression and enrichment in one call |
| A proteomics or antibody scientist | Peptide and protein inference, isotope envelopes, antibody numbering, chain typing and liabilities |
| A medicinal chemist | Conformers, tautomers, scaffolds, R-groups, matched pairs, chemical space and library screening |
| A builder of AI scientists | A tested, schema-typed scientific tool layer your agent can call instead of writing scripts |
🧰 Every tool
The full catalogue, regenerated from the live server every day. Open a section to see its tools.
🧬 Cloning & assembly · 33 toolsDigests, ligations, Gibson, Golden Gate, Gateway-style recombination, part grammars and assembly planning.
| Tool | What it answers |
|---|---|
Assemble index oligos assemble_index_oligos |
Turn index sequences into the oligos a synthesiser makes: each index spliced between 5'/3' adapter arms, or onto a PCR primer in either orientation with an optional spacer. |
Assemble operon assemble_operon |
What does an operon of these CDSs look like with a fresh RBS in front of each, designed against its real upstream context? |
Assembly plan simulate assembly_plan_simulate |
What final construct does a multi-level assembly plan give, each level's products becoming the next level's parts? |
Build assembly report build_assembly_report |
Build DnaCauldron's assembly report from an assembly result: the per-construct summary table, the constructs and errors spreadsheets as pandas-compatible CSV, and the Outcome / Number of assemblies stats. |
Check Golden Gate parts check_golden_gate_parts |
Which of each part's Type-IIS sites are the flanking sites the assembly needs and which are internal sites that will mis-cut it? |
Check methylation block check_methylation_block |
Does the host's methylation block these enzymes at each of their sites on this molecule? |
Classify grammar part classify_grammar_part |
Which Golden Braid, MoClo or Yeast ToolKit grammar, position and level does this record represent? |
Design fusion site primers design_fusion_site_primers |
Which primers add a Type-IIS site, spacer and chosen overhang to a part on a Tm-matched annealing footprint? |
Design Gibson primers design_gibson_primers |
Which primers amplify each fragment with the 5' overhang that fuses it to its neighbour, Tm-matched within each pair? |
Design multisite primers design_multisite_primers |
Which one-reaction QCLM primers make several mutations at once, with codons from an organism's usage table? |
Design mutagenesis primers design_mutagenesis_primers |
Which primers introduce this point change in a CDS by SOE-PCR or QuikChange? |
Design overhang set design_overhang_set |
Which overhang set of a given size ligates with high fidelity by measured data, keeping any junctions that cannot change? |
Design saturation primers design_saturation_primers |
Which overlapping primer pairs, one per site, carry a degenerate codon at every site in one reaction? |
Design split sites design_split_sites |
Where should one sequence be cut into Golden Gate fragments so that the overhangs the cuts create ligate efficiently and faithfully? |
Digest fragments digest_fragments |
Which fragments, with which ends, does a digest of this molecule produce? |
Digest reaction conditions digest_reaction_conditions |
Which buffer, temperature, cofactors and heat inactivation does a digest with these enzymes need, by NEB's own data? |
Domesticate part domesticate_part |
Which silent codon changes remove a part's internal Type-IIS sites without changing its protein? |
Draw gel draw_gel |
Where does each lane's fragments run on an agarose gel against the marker ladder? |
Find assemblies find_assemblies |
Resolve an organism to its published genome assemblies and the chromosomes, plasmids and organelles each one is made of, with every accession and length NCBI reports. |
Find restriction sites find_restriction_sites |
Where do these enzymes cut this molecule, on which strand, and what end does each cut leave? |
Find star sites find_star_sites |
Where else could these enzymes cut this molecule under star conditions, by REBASE's star-activity list and its one-base rule? |
Gibson assemble gibson_assemble |
What construct do these fragments make when they are joined by their terminal homology (Gibson, NEBuilder, In-Fusion)? |
Golden Gate assemble golden_gate_assemble |
What construct do these parts make in a Type-IIS (Golden Gate, MoClo) reaction? |
Ligate fragments ligate_fragments |
What products do these fragments make when their ends are ligated (after any per-fragment digest)? |
Plan thermocycler program plan_thermocycler_program |
Plan the cycling programme for an amplicon on a NAMED enzyme, and check the reaction against that manufacturer's own published limits. |
Protein digest protein_digest |
Which peptides, masses and m/z values does a proteolytic digest of this protein give? |
Rank strategies rank_strategies |
Which assembly chemistries can build a construct from these parts, and what does each cost and risk? |
Recombine recombine |
What products does a site-specific or homologous recombination between these molecules give (Gateway BP/LR, Cre/loxP, a serine integrase, homology arms, CRISPR knock-in)? |
Restriction ligate restriction_ligate |
What products survive a one-pot restriction-ligation, where re-formed sites are cut again? |
Run gel lane run_gel_lane |
Which bands, and in which DNA form, does a ladder, plasmid, digest or PCR lane of this molecule give? |
Run gel plate run_gel_plate |
Run a multi-lane virtual agarose gel and return its READING, not just its bands: how many lanes carrying how many bands over what range, positioned by which ladder, plus only the cautions this plate earned |
Score overhang fidelity score_overhang_fidelity |
What fraction of assemblies will ligate every junction correctly with this overhang set, by measured T4 ligase data? |
Scrub restriction sites scrub_restriction_sites |
Which fewest silent codon changes remove the forbidden restriction sites from a CDS? |
Primer design for every kind of PCR, melting temperatures and reaction simulation.
| Tool | What it answers |
|---|---|
Design bisulfite primers design_bisulfite_primers |
Which BSP or MSP primers work on the bisulfite-converted strands, and where are the CpG islands? |
Design CODEHOP design_codehop |
Which hybrid degenerate-core primers does a block of aligned protein give, for homologues too diverged for nucleotide design? |
Design degenerate primers design_degenerate_primers |
Which degenerate primers amplify every member of this aligned family, and how much of it does each cover? |
Design LAMP primers design_lamp_primers |
Which four core LAMP oligos, and optional loop primers, does this template give, judged against PrimerExplorer V5's criteria? |
Design primer pairs design_primer_pairs |
The Primer Designer's own ranked search: scan the record for primer pairs inside a product-size, Tm, length and GC window, score every candidate on Tm, dimers, hairpins, 3' stability, repeats, clamp and specificity un… |
Design primers design_primers |
Which primer pair amplifies this region, at what Tm, annealing temperature and cycling programme? |
Design sequencing primers design_sequencing_primers |
Which walk of primers reads this whole region, with what overlap, and what cannot be reached? |
Fusion PCR fusion_pcr |
What single product does overlap-extension PCR give from fragments that share terminal homology? |
Multiplex PCR multiplex_pcr |
What does a primer pool do on these templates: products, off-target binding, template-distinguishing pairs, and the dimer matrix? |
PCR amplify pcr_amplify |
What product does this primer pair amplify from the template? |
Primer check primer_check |
Where does a primer anneal on this molecule, and how well does each site match? |
Guide design and scoring, off-targets, screens, and editing outcomes measured from traces.
| Tool | What it answers |
|---|---|
CRISPR analyze screen crispr_analyze_screen |
Which genes are hits in a pooled CRISPR screen, by gene-level Bayes factor? |
CRISPR design guides crispr_design_guides |
Which CRISPR guides can be made against this target, and how good is each one on-target and off-target? |
CRISPR design library crispr_design_library |
Which oligos should be ordered for an sgRNA pool against these targets, with the vector's overhangs and optional barcodes? |
CRISPR quantify edits crispr_quantify_edits |
Quantify a CRISPR edit from a pair of Sanger traces |
CRISPR score DeepHF crispr_score_deephf |
Score CRISPR guides with DeepHF: a predicted knockout EFFICIENCY between 0 and 1 for wild-type SpCas9 (U6 or T7 promoter), eSpCas9(1.1) or SpCas9-HF1. |
CRISPR score DeepSpCas9 crispr_score_deepspcas9 |
Score CRISPR guides with DeepSpCas9 (Kim et al. |
Detect trace indel detect_trace_indel |
Ask whether a Sanger trace splits into TWO READS OF DIFFERENT LENGTH, which is what a heterozygous insertion or deletion does: clean up to the indel, then a superposition of two sequences offset by its length. |
Fold guide fold_guide |
Does a spacer base-pair into its sgRNA scaffold, and what does the whole guide RNA fold into? |
List sgRNA scaffolds list_sgrna_scaffolds |
Which sgRNA scaffolds has this workbench sourced, for which nucleases, from which publication? |
Peptide mass peptide_mass |
What is this peptide's monoisotopic and average mass, and its m/z at each charge? |
Protein signal peptide protein_signal_peptide |
Where would signal peptidase cut this protein, by von Heijne's weight matrix? |
Quantify base editing quantify_base_editing |
Quantify BASE EDITING from a single Sanger trace, with no control read |
Screen contamination screen_contamination |
Screen a nucleotide sequence for vector, adapter, linker and primer contamination against NCBI's UniVec, using VecScreen's own BLASTn parameters and category rules. |
Screen guides screen_guides |
Which guide spacers fail the pre-acceptance screens: GC, self-complementary hairpins, and hairpins against the sgRNA backbone? |
Screen molecule library screen_molecule_library |
Screen every structure of a library at once against drug-likeness rules and structural-alert catalogs, as the library grid does, and bin one rule property across it, split at the bound of a chosen rule. |
Screen oligo structure screen_oligo_structure |
Which oligos in a set form hairpins, self-dimers or cross-dimers, at any position and at the 3' end? |
Search off targets search_off_targets |
Which sites in this sequence could a guide also cut, and how specific is the guide within it? |
Survey off targets survey_off_targets |
How many off-target sites, by mismatch class, does each of these spacers have in this sequence? |
TIDE quantify indels tide_quantify_indels |
Quantify a CRISPR edit from a pair of Sanger traces by TIDE (Brinkman et al.) |
Trace reading, base calling, construct verification, read QC and alignment to a reference.
| Tool | What it answers |
|---|---|
Adopt trace calls adopt_trace_calls |
Replace a Sanger read's own base calls with TraceTuner's, on the trace, so the rest of the editor works from the re-called read: its sequence, its consensus, its verification against a reference, and every export. |
Call bases from trace call_bases_from_trace |
Call the bases of a Sanger trace from the signal, discarding the instrument's calls and deriving the bases, their positions and their quality from the peaks. |
Call mixed bases from trace call_mixed_bases_from_trace |
Call the bases of a Sanger trace AND ask at every position whether a second allele is present, writing a two-base IUB code (R, Y, S, W, K, M) where it is. |
Compare reads to reference compare_reads_to_reference |
Compare a SET of sequencing reads against one reference in ONE shared frame: align every read to the reference, vote a consensus column by column, and report the positions where the reads differ from it, each with the… |
Consensus from traces consensus_from_traces |
Merge one or two Sanger reads into a consensus with the ported SeqTrace caller. |
Demultiplex reads demultiplex_reads |
Which index did each read come from, and how many cannot be assigned reliably? |
Draw trace draw_trace |
Draw a window of a Sanger read as an SVG figure: the four dye traces over their called bases, the per-base Phred bars and a base ruler. |
Map reads map_reads |
Where on the reference does each read or contig align, with what MAPQ, as SAM? |
Read sequencing QC read_sequencing_qc |
Is a disappointing read the clone's fault or the run's, from the provider's coverage table or summary? |
Read structure consensus read_structure_consensus |
Which base pairs does a Stockholm alignment's consensus structure state, and how many aligned rows actually form each one? |
Recompute trace quality recompute_trace_quality |
Re-score a Sanger trace's own base calls from the signal, replacing the instrument's Phred values with ones measured from the peaks. |
Restore trace file calls restore_trace_file_calls |
Put an open Sanger read back on the base calls its FILE carries, undoing an adopted re-call. |
Trace raw signal trace_raw_signal |
The UNPROCESSED signal of a Sanger trace: how many scans the instrument recorded, where each channel's baseline sits, the peak raw value, and how many scans analysis discarded off the front as dye front. |
Trim reads trim_reads |
What do these FASTQ reads look like after the adapters and low-quality ends are trimmed, and how much was removed? |
Trim trace trim_trace |
Trim a Sanger read's low-quality ends, by either of the two methods that answer different questions: the instrument's own Mott record as written into the file, or a sliding mean-Phred window computed here. |
Verify construct verify_construct |
Compare a sequencing RESULT against the construct you designed and say what differs, where, and what it lands in. |
Verify read verify_read |
Does a sequencing read verify the reference, and which differences does it show? |
Amplification and melt curves, RDML runs, droplet gating, uncertainty and relative quantification.
| Tool | What it answers |
|---|---|
Analyze melt curves analyze_melt_curves |
What is each reaction's melting temperature, and does its melt show the product, an artifact, or no amplification? |
Bootstrap Cq bootstrap_cq |
How tightly do one reaction's observations pin down its Cq, efficiency and fitted coefficients? |
Call Cq call_cq |
What is each reaction's Cq and amplification efficiency, read off a fitted sigmoid under a named Cq definition? |
Classify droplets classify_droplets |
Which population (NN, NP, PN, PP) does each two-channel ddPCR droplet belong to, under a fixed grid, k-means or a k-nearest-neighbour vote? |
Design qPCR assay design_qpcr_assay |
Which primer pair and hydrolysis probe make a qPCR assay on this target, ranked by penalty? |
Gate droplets gate_droplets |
What is the template concentration in each ddPCR well, from the raw droplet amplitudes rather than the instrument's count? |
Melt profile melt_profile |
How does this molecule melt: the helicity curve, its Tm50, and the domains that melt together behind each HRM peak? |
Melting temperature melting_temperature |
The melting temperature of an oligo IN A BUFFER, UNDER A MODEL |
Propagate uncertainty propagate_uncertainty |
How uncertain is a reported qPCR quantity, given the uncertainty of each measurement in it, and which measurement contributes most? |
Quantify dPCR quantify_dpcr |
What is the absolute concentration of a target from digital PCR partition counts, with a confidence interval? |
Read RDML run read_rdml_run |
What does an RDML export hold, and what are one run's curves, Cq values, melts and partition counts as tables? |
Simulate TaqMan curve simulate_taqman_curve |
What amplification curve and Cq will a singleplex hydrolysis-probe qPCR assay draw, from its sequences and thermocycling programme? |
Codon optimisation, RBS and operons, probes, barcodes, genetic circuits and annotation.
| Tool | What it answers |
|---|---|
Annotate region annotate_region |
Say what a genomic region holds in the reference tracks: the genes and RefSeq transcripts it overlaps, which complete coding sequences it CONTAINS (the only case where a residue-level design is honest), the DGV struct… |
Audit barcodes audit_barcodes |
What minimum distance does this index set have, how many errors does that correct, and which subset survives a stricter budget? |
Audit CDS annotations audit_cds_annotations |
Does every annotated CDS of a map translate cleanly from its own bases and genetic code? |
Auto annotate auto_annotate |
Find and name known features on the subject |
Back translate back_translate |
Protein → DNA: the coding sequence that would encode a protein, weighted by a real codon-usage table. |
Build ENA submission build_ena_submission |
What flat file and manifest does ENA's Webin-CLI take for this record, and what would its validator refuse? |
Build GenBank submission build_genbank_submission |
What submission set (fasta with source modifiers and a feature table) does NCBI's table2asn take for this record, and what had to be refused or migrated? |
Calculate power calculate_power |
How many replicates does a planned test need to detect an effect, or what power, detectable effect or significance level does a fixed design give? |
Calculate rnaseq power calculate_rnaseq_power |
How many biological replicates, or how much sequencing depth, does an RNA-seq comparison need to detect a fold change in one gene? |
Check color balance check_color_balance |
Will the sequencer SEE these indexes? |
Check index pool check_index_pool |
Will this pool of sample indexes actually sequence? |
Check manufacturability check_manufacturability |
Does this sequence meet what a named synthesis vendor publishes it can make: length, GC, homopolymers and repeats? |
Check scorpion stem check_scorpion_stem |
Does a Scorpion probe's stem melt below the loop-target duplex by the margin the design needs? |
Codon optimality codon_optimality |
Frequency of optimal codons (Fop, Ikemura 1981) for an in-frame CDS against a real codon-usage table: what share of its codons are the ones a highly-expressed gene in that host would use. |
Codon table fetch codon_table_fetch |
Fetch a real codon-usage table for an organism and save it, so later steps can score against it by name. |
Codon usage analysis codon_usage_analysis |
How does this CDS's codon usage compare with an organism's: CAI, GC, rare codons, and the two reference-free bias measures? |
Codon usage distance codon_usage_distance |
How far is this region's codon usage from the record's other genes (CUFS)? |
Design barcodes design_barcodes |
Which index set of this size has a guaranteed minimum distance, and what does it actually correct? |
Design FREE codes design_free_codes |
Generate INDEL-correcting barcodes |
Design genetic circuit design_genetic_circuit |
Which characterised repressor gates compute this logic function, with what ON/OFF dynamic range, and what DNA does the circuit need? |
Design HCR probes design_hcr_probes |
Which HCR v3.0 split-initiator probe pairs tile this target within their composition and free-energy windows? |
Design ish probes design_ish_probes |
Which oligo set images this target best: tiled candidates meeting Tm, GC and composition, screened for off-target binding and gathered into a set? |
Design knockout package design_knockout_package |
What does a complete knockout or knock-in build need: guides, an off-target census, a repair template with arms, screening primers outside the arms, the protocol, and what to buy? |
Design oligo plate order design_oligo_plate_order |
In which wells, in the supplier's own fill order, does an oligo set go on a plate order? |
Design padlock probes design_padlock_probes |
Which padlock probes target this transcript for in-situ sequencing, and which junctions could be ligated on another transcript? |
Design RBS design_rbs |
Which 5'UTR puts a CDS's translation initiation at a target strength? |
Discover annotation contradictions discover_annotation_contradictions |
Which signal peptides or transmembrane segments in reviewed human UniProt does a sequence predictor contradict? |
Discover codon outliers discover_codon_outliers |
Which genes of a genome use synonymous codons in a way the genome's own average does not explain? |
Estimate effect size estimate_effect_size |
How large is the effect in pilot data, standardised, with a confidence interval, ready to size the full experiment? |
Export barcodes export_barcodes |
What does this index set look like as an order sheet, a FASTA, a SampleSheet, or the actual oligos? |
Optimize sequence optimize_sequence |
What sequence satisfies these constraints and scores best on these objectives? |
Rank next tests rank_next_tests |
Which candidate experiment would teach the most about the hypothesis it is registered against, and how much of it is worth running? |
Rank tradeoffs rank_tradeoffs |
Which candidates in a table does no other candidate beat on every objective at once, how deep does each of the rest sit, and which candidate beats it? |
Score RBS score_rbs |
How strong is the ribosome-binding site already in front of this start codon, and what sets that strength? |
Tree taxon annotations tree_taxon_annotations |
What does this NeXML file say about each of its taxa? |
Pairwise and multiple alignment, dot plots, model selection, trees and tree comparison.
| Tool | What it answers |
|---|---|
Align read align_read |
How does one sequencing read align to the reference, as two gapped rows? |
Align sequences align_sequences |
How do these sequences line up column by column, by partial-order alignment (a pile of reads over one locus) or progressive alignment (a family of homologous genes)? |
Alignment agreement alignment_agreement |
Read an alignment window and say how well its reads agree with the reference underneath them, the way the pileup's own bar does: the compared and differing base counts, plus the RefSeq gene models and known dbSNP vari… |
Alignment window alignment_window |
Read one window of a BAM or SAM: its reads, the depth across it, and what the pairs say about the library |
Build tree build_tree |
What phylogeny do these aligned sequences support, under a distance, parsimony, maximum-likelihood or Bayesian method, with branch support? |
Compare trees compare_trees |
How far apart are these trees over the same taxa, and what topology do they share? |
Discover gene tree discordance discover_gene_tree_discordance |
Which genes' own alignments reject the species tree (Shimodaira-Hasegawa test against its nearest-neighbour rearrangements)? |
Discover tree incongruence discover_tree_incongruence |
Do some loci of a multi-locus alignment have a different history from the rest (incongruence length difference test)? |
Dot plot dot_plot |
Where does this sequence resemble itself or another, as a dot plot of repeats, inversions and shared regions? |
Dot plot grid dot_plot_grid |
Which members of this sequence set share material with which, as an all-against-all grid of dot plots? |
Draw alignment draw_alignment |
What does this window of an alignment look like as a figure? |
Draw tree draw_tree |
What does this tree look like as a figure? |
EBI align ebi_align |
Run a sequence through EMBL-EBI's Job Dispatcher: Clustal Omega, MUSCLE, MAFFT, Kalign, T-Coffee, EMBOSS needle/water/matcher/stretcher, LALIGN, phmmer, hmmscan, PSI-BLAST or Phobius. |
Export tree export_tree |
What does this tree look like in Newick, NEXUS, PhyloXML or NeXML? |
Select substitution model select_substitution_model |
Which substitution model do these data prefer, by AIC, AICc or BIC with Akaike weights? |
Transform tree transform_tree |
What does this tree look like re-rooted, pruned, ladderized, or with weak branches collapsed? |
Tree statistics tree_statistics |
What shape does this tree have: tips, height, balance, the gamma statistic, lineages through time, and the patristic distances? |
Variant calls, copy-number segmentation, LOH and mosaicism, genome regions.
| Tool | What it answers |
|---|---|
Apply variant call apply_variant_call |
Substitute one called ALT allele into a sequence and return the edited bases, the range the edit occupies and the length change. |
Browse region browse_region |
Read one window of a genome the way a genome browser shows it: the cytogenetic bands it spans, the transcripts in the chosen RefSeq set, which residues of each protein the window encodes (translated from the assembly’… |
Check invariants check_invariants |
Is this designed sequence admissible: protein unchanged, forbidden sites absent, frame intact, length, GC and CAI within bounds? |
Copy number allele split copy_number_allele_split |
Read an Affymetrix array result's own allele-specific copy number: for each segment the major and minor allele counts (1+1, 2+0, 0+0), what they mean (balanced, allelic imbalance, loss of heterozygosity placed against… |
Copy number compare copy_number_compare |
Join two Affymetrix copy-number samples' own calls and report which events they share and which only one of them carries: for every pair, the chromosome both files resolved to, the kind, the bases they overlap and the… |
Copy number findings copy_number_findings |
Scan every indexed chromosome of an Affymetrix copy-number container and report what the file itself called: gains, losses and stretches of homozygosity, with their positions, marker counts and spans, plus a per-chrom… |
Copy number loh copy_number_loh |
Recompute loss of heterozygosity from an Affymetrix array's own per-marker genotype calls, rather than reading the runs the producer wrote: APT's window method, with the false-positive rate and the assumed genotyping… |
Copy number mosaicism copy_number_mosaicism |
Estimate which mosaic fraction class each region of one chromosome is closest to, as Affymetrix Power Tools computes it. |
Copy number read copy_number_read |
Read an Affymetrix copy-number container (CNCHP/CYCHP/OSCHP/CHP) and say what is in it: the algorithm and array that produced it, its data sets and their graphs, the per-chromosome marker index the file carries, and |
Copy number regions copy_number_regions |
Place an Affymetrix copy-number sample's own calls in ClinGen's curated regions: for each region, which gains, losses or stretches of homozygosity fall in it, at what reciprocal overlap, and how much of the region the… |
Copy number segment copy_number_segment |
Segment one chromosome of an Affymetrix copy-number container by up to four independent methods and report where they agree. |
Copy number somatic copy_number_somatic |
Read an Affymetrix array result's own somatic-mutation calls: one row per mutation probe set with the producer's call, the score behind it and the two thresholds that call was graded against. |
Design expression variants design_expression_variants |
Which codon-optimised variants of this CDS does an expression trial need, and how do they differ? |
Lookup variant lookup_variant |
Look up a variant: ClinVar clinical interpretation, dbSNP records, gnomAD population frequency and gene constraint, CADD deleteriousness, or GWAS/eQTL associations. |
Population ancestry population_ancestry |
What mixture of K ancestral populations does each sample look like, and which K does cross-entropy prefer? |
Population Fst population_fst |
How differentiated are these populations, per site and averaged, with a jackknife standard error? |
Population site stats population_site_stats |
What are this call set's per-site and per-sample genotype statistics, including heterozygosity, F and the exact Hardy-Weinberg test? |
Read variant calls read_variant_calls |
Read a variant call set (VCF, bgzipped VCF or BCF) and return the records matching a query: a locus, a variant class, a QUAL floor, PASS-only, a sample that is not hom-ref, or an INFO key. |
Score variant effect score_variant_effect |
Score protein substitutions with ESM-2, the zero-shot way facebookresearch/esm's own predict.py does: how much less (or more) likely the mutant residue is than the wild type at that site, under a protein language model. |
Variant call summary variant_call_summary |
Summarize a variant call set the way bcftools stats does: records by class, transitions and transversions with their ratio, the twelve directed substitutions, indel lengths, per-contig counts, the FILTER tally, the QU… |
Domains and motifs, residue sites, protein properties and peptide evidence.
| Tool | What it answers |
|---|---|
Antibody antigen contacts antibody_antigen_contacts |
Which antibody residues touch which antigen residues in this complex, how close, and what kind of interaction is each? |
Antibody isotype antibody_isotype |
Which immunoglobulin gene and allele is this chain's constant region, and where does each IMGT domain sit on it? |
Antibody liabilities antibody_liabilities |
Which sequence liabilities does this variable domain carry, and in which IMGT region does each sit? |
Antibody molecule antibody_molecule |
What are an assembled Fab's or IgG's mass, isoelectric point, charge at a pH, and extinction coefficient reduced and oxidised? |
Bayesian protein inference bayesian_protein_inference |
What is the posterior probability that each protein, group and match is present? |
DELTA BLAST SMART delta_blast_smart |
DELTA-BLAST, run on this machine: build a position-specific profile for a protein from the SMART conserved domains it contains, then search other proteins with it (one PSI-BLAST iteration) |
Find linear motifs find_linear_motifs |
Short linear motifs in a protein: degrons, docking sites, targeting signals, cleavage and modification sites |
Graft antibody CDRs graft_antibody_cdrs |
Which human germline framework accepts this domain's CDRs, and what is the grafted sequence? |
Humanize antibody humanize_antibody |
Which framework mutations does Sapiens make to humanize this variable domain, keeping the parental CDRs? |
Infer proteins infer_proteins |
Which proteins do these peptide-spectrum matches support, and which cannot be told apart? |
Lookup protein lookup_protein |
Look up a protein: UniProt records, InterPro/Pfam domain architecture, STRING interaction networks, Human Protein Atlas expression, or a predicted/experimental structure from AlphaFold, PDB or EMDB. |
Lookup residue sites lookup_residue_sites |
The individual catalytic, substrate-binding, metal-binding and interface residues a member database annotates INSIDE a domain, for a known protein. |
Number antibody number_antibody |
Which antibody or TCR variable domains does this protein carry, how are they numbered, and which germlines are closest? |
Protein disorder protein_disorder |
Which stretches of this protein does FoldIndex predict unfolded? |
Protein disorder metapredict protein_disorder_metapredict |
What is this protein's per-residue disorder score, and which regions are IDRs, by metapredict? |
Protein membrane profile protein_membrane_profile |
Which windows of this protein look transmembrane, globular or surface-seeking on an Eisenberg hydrophobic-moment plot? |
Protein profile protein_profile |
How does a chosen physicochemical scale vary along this protein? |
Protein properties protein_properties |
What are this protein's mass, formula, isoelectric point, instability index and amphipathicity? |
Protein topology protein_topology |
Which residues of this protein are inside, in a transmembrane helix, or outside, by the HMM-TM model? |
RPS BLAST CDD rps_blast_cdd |
RPS-BLAST a protein against NCBI's Conserved Domain Database (CDD) or one of its member collections (Pfam, SMART, COG, KOG, PRK, TIGR, NCBI-curated), through NCBI Batch CD-Search. |
RPS BLAST SMART rps_blast_smart |
rpsblast, run on this machine: find conserved domains in a protein against NCBI's SMART domain models (1,011 PSSMs from CDD). |
RPSTBLASTN SMART rpstblastn_smart |
rpstblastn, run on this machine: find conserved domains in DNA by searching all six reading frames against NCBI's SMART domain models (1,011 PSSMs from CDD). |
Scan motif sites scan_motif_sites |
Where does a transcription-factor matrix match this sequence, on either strand, at a threshold set as a fraction of that matrix's own score range? |
Scan protein domains scan_protein_domains |
De-novo protein domain and family annotation: submits a protein to EMBL-EBI InterProScan and returns every member-database signature that matches it |
Molecules, conformers, scaffolds, reactions, chemical space and library screening.
| Tool | What it answers |
|---|---|
Activity cliffs activity_cliffs |
SALI activity cliffs (Guha & Van Drie 2008) in a list of small molecules with one activity each: every pair scored as the activity difference over one minus the Tanimoto similarity of RDKit path fingerprints, steepest… |
Assess small molecule assess_small_molecule |
Assess a small molecule given as SMILES or a molfile: RDKit's descriptors, medchem's drug-likeness rules (Lipinski, Veber, Ghose, Egan, REOS, rule of three, CNS and more) and the papers' own readings where medchem dep… |
Canonical tautomer canonical_tautomer |
A small molecule's tautomers and the canonical one, as RDKit's TautomerEnumerator finds and scores them: 37 hydrogen-shift transforms (after MolVS and Sitzmann 2010), scored by aromatic rings, twelve weighted groups a… |
Cluster molecules cluster_molecules |
Cluster or diversity-pick a list of small molecules on 1 − Tanimoto of Morgan radius-2 fingerprints: Butina sphere exclusion (RDKit ClusterData, optional reordering), MaxMin diversity picking (RDKit MaxMinPicker, seed… |
Compare molecules compare_molecules |
How similar two small molecules are: Tanimoto under six RDKit fingerprints (Morgan/ECFP4, atom pair, topological torsion, RDKit path, pattern, MACCS), every DataStructs metric (Tanimoto, Dice, cosine, Sokal, Russell,… |
Decompose r groups decompose_r_groups |
RDKit's R-group decomposition of a list of small molecules on a core given as SMARTS (default RGroupDecomposition parameters): per matched structure its core and substituents R1, R2 …, and the structures the core does… |
Enumerate protonation states enumerate_protonation_states |
Enumerate a small molecule's protonation states across a pH window with Dimorphite-DL (Ropp et al. |
Enumerate reaction enumerate_reaction |
Run a reaction SMARTS over lists of reactants, every combination, with RDKit's reaction engine: one list per reactant template, in template order. |
Generate conformers generate_conformers |
3D conformers of a small molecule by OpenChemLib's torsion-library generator, each scored and optionally minimized under MMFF94, MMFF94s or MMFF94s+ (whose MMFF94 equals Halgren's OPTIMOL on all 761 validation-suite s… |
Lookup compound lookup_compound |
Look up a chemical compound or drug: ChEMBL molecules, mechanisms of action and bioactivity, PubChem properties, ChEBI ontology, Rhea reactions, or purchasable ZINC compounds. |
Map chemical space map_chemical_space |
Principal components of a list of small molecules, computed as R's prcomp computes them, on the scaled property table or on Morgan radius-2 bits: each structure's scores on PC1 and PC2, every component's standard devi… |
Map reaction atoms map_reaction_atoms |
Predict which reactant atom each product atom came from (atom-to-atom mapping) with RXNMapper (Schwaller et al., Sci. |
Matched molecular pairs matched_molecular_pairs |
Matched molecular pairs (Hussain & Rea 2010) in a list of small molecules, as mmpdb finds them: pairs that differ by one change no larger than a heavy-atom limit, grouped by the change as a reaction SMIRKS, most pairs… |
Scaffold network scaffold_network |
The scaffold network (Kruger et al. |
Search molecule library search_molecule_library |
Which of a list of small molecules contain a SMARTS substructure, with RDKit's substructure library (pattern-fingerprint screen, then atom matching). |
Write structure library write_structure_library |
Write a list of small molecules as one file: SDF (V2000 or V3000), each record named and, optionally, carrying its canonical SMILES and RDKit descriptors as data fields; or SMILES or CXSMILES, one record a line follow… |
Differential expression, gene-set enrichment and falsification-tested discovery programmes.
| Tool | What it answers |
|---|---|
Describe discovery corpus describe_discovery_corpus |
What does a discovery corpus hold, before any test is run on it? |
Differential expression differential_expression |
Differential expression from raw RNA-seq read counts, by one of the three standard count models. |
Discover flag rates discover_flag_rates |
How often does a corpus of maps carry a cryptic promoter, splice site or synthesis-breaking repeat more extreme than chance? |
Discover reference concordance discover_reference_concordance |
Does a reference-gene stability ranking hold across conditions, and which candidates rank well everywhere? |
Discover reference stability discover_reference_stability |
Are candidate reference genes more or less variable across human tissues than genes of the same abundance? |
Discover site avoidance discover_site_avoidance |
Which exact restriction sites does each sequence carry far less, or far more, often than a stated null predicts? |
Discover target validation discover_target_validation |
Does the evidence in a set of gene-level tables support a hypothesis that one gene drives a phenotype, by sequential falsification? |
Gene set enrichment gene_set_enrichment |
Preranked gene set enrichment analysis (GSEA; Subramanian et al. |
Gene set overrepresentation gene_set_overrepresentation |
Over-representation analysis (ORA): which gene sets hold more of a gene list than chance, by the one-sided hypergeometric test against a background, as clusterProfiler's enricher() runs it (enrichit 0.2.6). |
Run discovery programme run_discovery_programme |
Which pre-registered hypotheses does a programme of falsification tests support, with the false discovery rate controlled across all of them? |
Validate gene trait validate_gene_trait |
Does public expression and GWAS evidence support a hypothesis that a gene is involved in a trait, by sequential falsification? |
Search and fetch from NCBI, EMBL-EBI, UCSC, UniProt and more, then hand the record to any tool.
| Tool | What it answers |
|---|---|
Apply feature file apply_feature_file |
Put the features from a GTF onto the record. |
Cancel research run cancel_research_run |
Which pending hypotheses of a research run should never run? |
Fetch record fetch_record |
Fetch a sequence by accession from an authoritative archive (NCBI Nucleotide or Protein, ENA, UniProtKB, the iGEM Registry, Addgene, or the EBI Dbfetch gateway) and hand it downstream as a real record with its annotat… |
History protocol history_protocol |
What numbered bench protocol does a construct's build history describe? |
List databases list_databases |
The authoritative databases available, with what each one covers, whether it is reachable from the browser, and any license or coverage caveat. |
List samples list_samples |
Browse the bundled sample library: the real bio files a new project can start from (GenBank and SnapGene plasmids, FASTA sets, alignments, Sanger traces, structures, variant calls and more), each with its id, format a… |
Lookup clinical lookup_clinical |
Look up clinical and translational evidence: ClinicalTrials.gov trials, FDA labels and adverse events, Open Targets associations, CIViC cancer variant evidence, ClinGen curation, cBioPortal cohorts, or DepMap dependen… |
Lookup gene lookup_gene |
Look up a gene or genomic region: Ensembl records, cross-references, MyGene identifiers, UCSC assembly data, GTEx expression, or BioMart tables. |
Lookup omics lookup_omics |
Look up omics and regulation records: GEO and ArrayExpress experiments, PRIDE proteomics, MetaboLights, MGnify, ENCODE experiments and files, JASPAR motifs, or UniBind TF binding sites. |
Lookup ontology lookup_ontology |
Resolve an ontology term, pathway or cell type: OLS ontologies, QuickGO annotations, Reactome pathways, KEGG entries, Rfam RNA families, CellGuide/PanglaoDB cell types and markers, or an antibody RRID. |
Notebook cross refs notebook_cross_refs |
Which plasmids, actions and gels does a notebook entry refer to? |
Query database query_database |
Ask one of the ~60 authoritative databases a question and hand its rows downstream |
Research run status research_run_status |
What state is a research run in, and what would resuming it do? |
Resume research run resume_research_run |
What verdicts does a research run reach once its failed, deferred and never-attempted hypotheses have run? |
Search literature search_literature |
Search the published literature: PubMed, Europe PMC (including open-access full-text sections), OpenAlex, Crossref, arXiv, bioRxiv/medRxiv preprints or DataCite datasets. |
Search records search_records |
Search the sequence archives by free text (a gene name, a protein, an organism, a phrase) across NCBI Nucleotide and Protein, ENA (plain records, WGS and TSA/TLS assembly sets, and annotated coding/non-coding features… |
Everything else a bench scientist asks of a sequence.
| Tool | What it answers |
|---|---|
BLAST project sequences blast_project_sequences |
Search a sequence against your own records with blastn or blastp, on this machine: the local database is built from every project record of the program's alphabet, and every E-value is computed from that database's ow… |
BLAST search blast_search |
Search a sequence against NCBI BLAST+ at EMBL-EBI (blastn, blastp, blastx, tblastn or tblastx) over ENA, UniProtKB, PDB and the vector-screening sets. |
Check assay decay check_assay_decay |
How often do a published assay's oligos mismatch the genomes circulating now, and where in each oligo do the mismatches sit? |
Check primer specificity check_primer_specificity |
Check primer pairs for products off their template, the way NCBI Primer-BLAST does, and rank them by it: each distinct primer is searched against a sequence database at EMBL-EBI with short-query BLAST, hits are paired… |
Check rows check_rows |
Does every row of this table satisfy the rule, and which rows broke it? |
Enzyme cut counts enzyme_cut_counts |
How many times does each enzyme cut this molecule? |
Filter items filter_items |
Which rows of this table meet the condition, and how many were dropped? |
Find ORFs find_orfs |
Which open reading frames does this molecule carry, on both strands? |
Find primer SNPs find_primer_snps |
Find known SNPs under primers, the check NCBI Primer-BLAST makes with "Primer binding site may not contain known SNP". |
Fold RNA fold_rna |
What is the minimum-free-energy secondary structure of this sequence, and its free energy? |
Fragment ions fragment_ions |
Which theoretical fragment ions does this peptide give, at each charge? |
GC content gc_content |
What is this sequence's GC fraction, overall or along a sliding window? |
Genotype PCA genotype_pca |
What population structure do these genotypes show in their principal components? |
Isotope envelope isotope_envelope |
What coarse isotope pattern does this peptide or formula show: the heights and masses of M, M+1, M+2 and beyond? |
Isotopic composition isotopic_composition |
Which isotopic composition is this peptide most likely to carry, and how abundant is it? |
Linkage disequilibrium linkage_disequilibrium |
How much linkage disequilibrium is there between each pair of biallelic sites, and which sites survive pruning? |
Load trace load_trace |
Read a Sanger trace (.ab1 / .scf / .ztr) and hand its BASE CALLS onward as a record, with the per-base quality and the trim bounds beside them. |
Mask sequence mask_sequence |
Mask the parts of a sequence a similarity search should not seed on, using BLAST's own three maskers: DUST for compositionally biased DNA (poly-A, simple repeats), SEG for the protein equivalent, and WindowMasker for… |
Match part by sequence match_part_by_sequence |
Identify a stretch of DNA by asking the iGEM Registry which published part carries exactly those bases, and hand back that part's own description, Sequence-Ontology role, literature citation and license. |
MIQE checklist miqe_checklist |
Which MIQE 2.0 items does a qPCR paper provide, and where, or why are they omitted? |
Rank reference genes rank_reference_genes |
Which candidate reference genes are most stable on this plate, by geNorm, NormFinder, BestKeeper, comparative delta-Ct and their consensus? |
Read MGF read_mgf |
What spectra does this MGF file hold? |
Read mzML read_mzml |
What spectra, precursors and acquisition metadata does this mzML run hold? |
Read structure read_structure |
What is in this structure file: chains, sequences, ligands, solvent, disulfides, modified residues, B-factors, cell, resolution and experiment? |
Record composition record_composition |
What is this record made of: molecular weight under its own topology, GC and AT, and the per-symbol census? |
Relative expression relative_expression |
How much does a gene's expression change between groups, by delta-delta-Ct, delta-Ct or the standard-curve model, with a significance test on request? |
Reverse complement reverse_complement |
What is the reverse complement of this sequence, with its annotations carried over? |
Scan intrinsic terminators scan_intrinsic_terminators |
Which rho-independent terminators does this bacterial sequence carry, and how good is each hairpin and tail? |
Scan sigma70 promoters scan_sigma70_promoters |
Which sigma70 promoters does this bacterial sequence carry, and how strong is each by the La Fleur-Hossain-Salis biophysical model? |
Scan splice sites scan_splice_sites |
Which splice donors and acceptors does this sequence spell, by maximum-entropy strength and by typicality against measured Arabidopsis sites? |
Score spectrum score_spectrum |
How well does this MS/MS spectrum match this peptide, by X!Tandem HyperScore? |
Size fragments size_fragments |
Size the peaks of a fragment-analysis run (.fsa / .hid) against its own size standard, and hand them on as lengths in bases. |
Summarize rows summarize_rows |
What is this table column's summary: its largest, smallest, median, mean or spread, overall or per group? |
Target decoy qvalues target_decoy_qvalues |
What q-value does each peptide-spectrum match get by target-decoy competition, and how many pass a threshold? |
Translate sequence translate_sequence |
What protein does this DNA encode, under the genetic code chosen? |
Chain tools into reproducible workflows, export records, keep lab notes.
| Tool | What it answers |
|---|---|
Build addgene deposit build_addgene_deposit |
Fill Addgene's own deposit spreadsheet from a record: one row per plasmid with its name and sequence, plus your answers for every plasmid (purpose, plasmid type, cloning method, resistance, growth strain and the other… |
Compare constructions compare_constructions |
Align two constructs' build procedures step by step, in order |
Enzyme collection enzyme_collection |
Resolve one of your saved enzyme collections to the enzyme names in it, so a later step can scan, digest or design with 'my Golden Gate set' by name instead of whatever happens to be selected. |
Export construction record export_construction_record |
Write a construct's recorded build out as a document: a methods section, a step spreadsheet, the full decoded record, the molecule carrying its own history as GenBank qualifiers, the whole strategy as an OpenCloning d… |
Export map SVG export_map_svg |
What does this molecule's circular map look like as a publication figure? |
Export trace export_trace |
Write a Sanger read out in any of the eight formats the trace editor's Export section offers, and hand the file back as TEXT in the pipeline rather than as a download. |
Get construction history get_construction_history |
What a construct was BUILT from: the recorded operations, the molecules they consumed, how many rounds deep the build goes, and which of the 5 sources the record came from. |
List workflow templates list_workflow_templates |
The built-in starter workflows |
Plan rnaseq experiment plan_rnaseq_experiment |
For an RNA-seq experiment testing thousands of genes at a target false discovery rate, how many biological replicates per group are needed, and what power does a given number give? |
Remember lab preference remember_lab_preference |
Remember what this lab uses, so the PCR program, primer design and codon optimization start on it: the polymerase, the primer length and GC windows, and the expression host. |
Run workflow run_workflow |
Run a workflow graph: nodes naming tools, wires carrying one node’s output into another’s input, $whenExpression to make a step conditional, and scatter to run a step once per element of a list. |
Save enzyme collection save_enzyme_collection |
Save a set of enzymes as a named collection in your Enzyme Collections panel, so a scan that found the enzymes worth keeping ends by keeping them instead of asking you to retype the list. |
Validate workflow validate_workflow |
Would this workflow graph run? |
❓ FAQ
Do I need an account or an API key? No. Add the URL and go.
Is my data stored? No. The server is stateless and keeps nothing between calls. A few tools querypublic databases (NCBI, EMBL-EBI, UCSC, UniProt) with exactly the query you asked for.
Which assistants work? Any MCP client: Claude, Claude Code, ChatGPT, Cursor, VS Code, Windsurf,Cline, and agent frameworks that speak MCP.
How do I know a result is right? Every result names the method, parameters and inputs behind it,and each engine is tested against the reference implementation of its field before it ships. If youfind a wrong answer, open an issue: wrong answersare treated as bugs.
Is there a visual interface? Yes. The same engine runs in your browser atjeanslabs.vercel.app: a plasmid and sequence editor with cloningsimulation, primer design, gel and Sanger views. Free, no account.
About
Jean (said like gene) is proprietary software by Melad Labs, © Melad Labs, all rightsreserved, offered as the hosted service above. This repository is its public listing and holds nosource code. The registry entry io.github.genmnz/jean and the catalogue above are kept currentautomatically.
Keywords: MCP server · Model Context Protocol · remote MCP · scientific computing · life sciences ·bioinformatics · computational biology · molecular biology · synthetic biology · genomics · lab software ·DNA · RNA · protein · plasmid · plasmid map · vector design · molecular cloning · in silico cloning ·restriction digest · ligation · Gibson assembly · Golden Gate · MoClo · Gateway cloning · site-directedmutagenesis · PCR · primer design · melting temperature · Tm calculator · qPCR · RT-qPCR · ΔΔCq ·digital PCR · ddPCR · LAMP · bisulfite sequencing · degenerate primers · CRISPR · Cas9 · sgRNA design ·off-target · base editing · Sanger sequencing · chromatogram · NGS · sequence alignment · MSA ·phylogenetics · maximum likelihood · variant calling · VCF · copy number · population genetics · Fst ·differential expression · gene set enrichment · proteomics · mass spectrometry · antibody numbering ·structural biology · cheminformatics · drug discovery · codon optimization · RBS design · geneticcircuits · DNA barcodes · GenBank · FASTA · RDML · NCBI · EMBL-EBI · UCSC · UniProt · AI for science ·AI scientist · lab copilot · Claude connector · ChatGPT app · Cursor · VS Code
