bots.st/jean-molecular-biology-genomics
Jean — Molecular Biology & Genomics
Molecular biology and genomics analysis tools
2590 ms
answered our call
- State
- Answered
- Protocol
- MCP 2025-06-18
- Tools listed
- 200
- Answered
- 3 of the last 3 calls
How to reach it
- MCP, HTTP
https://jeanslabs.vercel.app/mcp
What it can do
| Tool | What it says it does |
|---|---|
align_read | Pairwise-align ONE sequencing read against a reference and hand on the two gapped rows, so the read can be graded. |
align_sequences | Multiple-sequence alignment over several sequences, under either of TWO engines that answer different questions and neither of which is a fallback for the other. |
alignment_pca | Principal component analysis of the rows of an alignment: the pairwise similarity of every two rows under PID or a substitution matrix (BLOSUM62, PAM250 for protein; Jalview's DNA matrix for nucleotides), decomposed into eigenvectors, and each row's coordinate on the leading components, so rows… |
alignment_redundancy | Find the rows of an alignment that repeat another: each row's redundancy is its highest percent identity to a row at least as long (ungapped residues), and a row at or above the threshold is redundant, so filtering keeps the longest representative of each near-identical group. |
analyze_melt_curves | Melt curves to melting temperature, under any of THREE engines that answer different questions and none of which is a fallback for another. |
antibody_antigen_contacts | Type the ANTIBODY-ANTIGEN INTERFACE of a deposited complex: which residue of each antibody chain touches which residue of the antigen, how close, and what kind of interaction each pair makes - ionic, polar, weak polar, hydrophobic, aromatic, carbonyl, or a disulfide. |
antibody_canonical_classes | Assign each CDR of an antibody heavy, kappa or lambda variable domain to its canonical structure class: SCALOP's length-independent clusters of known loop conformations (CDR-H1, H2, L1, L2, L3; H3 has no canonical classes). |
antibody_isotype | Name the CONSTANT region of an antibody chain: which immunoglobulin gene and allele it carries (IGHG1, IGHA2, IGKC, IGLC2 …), and where each IMGT domain sits on it — CH1, the hinge, CH2, CH3, the secretory tail and the membrane exons, or the single C region of a light chain. |
antibody_liabilities | Scan antibody and TCR variable domains for sequence liabilities (Asn deamidation, Asp isomerization, N-glycosylation sequons, Asp-Pro cleavage, Met and Trp oxidation, unpaired or missing conserved cysteines), each placed in its IMGT region so CDR hits can be told from framework ones. |
antibody_molecule | Properties of an assembled antibody from its heavy and light chains: molecular weight, isoelectric point, net charge at a pH, and the extinction coefficient and A280 with cysteines reduced and with every pair formed into a cystine, for a Fab (1 heavy + 1 light) or an IgG (2 + 2). |
antibody_position_frequencies | How common each residue of an antibody variable domain is at its IMGT position, and which residues are rarer there than a cut (abYsis's 1% "unusual residue" by default). |
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_multiple_inserts | Open ONE circular backbone at several places and place several inserts in a single step. |
assemble_operon | Stack several CDSs into one contiguous operon, designing a fresh ribosome-binding site in front of each one AGAINST ITS REAL UPSTREAM CONTEXT — which is why the RBS for gene 2 is not the RBS design_rbs would give it in isolation. |
assembly_plan_simulate | Run a MULTI-LEVEL assembly plan (DnaCauldron `AssemblyPlan`): several assemblies arranged into dependency levels, where each level's products become parts for the next. |
audit_barcodes | Check an index set you ALREADY have, rather than designing a new one: the minimum distance between any two, how many errors that guarantees correcting, the full distance matrices, and — optionally — the subset that survives pruning to a stricter error budget. |
audit_cds_annotations | Check every annotated CDS of one or more GenBank maps against its own bases and genetic code: a frame that does not close (frameshift), a stop inside the reading frame, a first codon the code cannot start with, a last codon that is not a stop, and a /translation the bases do not give. |
bayesian_protein_inference | Bayesian protein inference, Epifany (validated against OpenMS BayesianProteinInferenceAlgorithm on PXD000001): the posterior probability that each protein, each indistinguishable group and each peptide-spectrum match is present, from the matches' posterior error probabilities under a network in… |
bootstrap_cq | Resampling error bars on ONE reaction's Cq. A Cq is read off a fitted model, so its uncertainty is how tightly the observations pin that model down - which propagating a measured spread cannot answer. |
build_ena_submission | Turn a record into what ENA's Webin-CLI takes for an annotated sequence (`-context sequence`): an ENA flat file (`.embl`) and its manifest. |
build_genbank_submission | Turn a record into the SUBMISSION SET NCBI's `table2asn` consumes: a `.fsa` whose defline carries the source modifiers, and a 5-column feature table (`.tbl`) beside it. |
build_tree | Build a phylogeny from aligned sequences — distance methods (NJ, BIONJ, FastME, UPGMA/WPGMA), parsimony, maximum likelihood, or Bayesian MCMC under a strict clock and coalescent prior — with branch support from a bootstrap, aLRT or aBayes, or, for the Bayesian method, clade posterior… |
calculate_power | Power and sample size for a planned experiment: how many replicates a test needs to detect an effect, or what power, detectable effect or significance level a design that is already fixed gives. |
calculate_rnaseq_power | Sample size and power for an RNA-seq comparison of two groups, one gene at a time: the biological replicates per group needed to detect a fold change at a given sequencing depth and within-group coefficient of variation, or the power, detectable fold change, CV or α a fixed design gives. |
call_cq | Amplification curves to Cq, one row per reaction. Fits each raw fluorescence curve to a sigmoid (l4-l7, b4-b7), reads the Cq off it under any of the seven definitions (cpD1, cpD2, maxE, expR, Cy0, CQ, maxRatio) or at a fluorescence threshold you set (the classic Ct), and returns the per-reaction… |
check_assay_decay | Check a published PCR or sequencing assay against the sequences that are circulating now: for each oligo, where its best binding site is in each genome, how many positions mismatch, and whether a mismatch sits in the 3′ end a polymerase has to extend through. |
check_color_balance | Will the sequencer SEE these indexes? Per-cycle channel occupancy for a set of index sequences under an instrument's own SBS chemistry, checked against Illumina's rules (no dark cycle, both channels preferred, no GG in the first two cycles), each violation citing the vendor article it comes from —… |
check_golden_gate_parts | Check parts BEFORE a Type-IIS assembly: how many recognition sites each carries, which of them are the two deliberate flanking sites and which are internal sites that will mis-cut the part. |
check_index_pool | Will this pool of sample indexes actually sequence? One verdict over the indexes a lab is about to load: duplicates, uniform length, the distance the set really guarantees against the distance it claims, per-cycle color balance on the chosen instrument's own chemistry, the index-2 orientation that… |
check_invariants | Decide whether a sequence is scientifically admissible: protein unchanged, forbidden restriction sites absent, reading frame intact, length/GC/CAI inside stated bounds. |
check_manufacturability | Measure a sequence against what a NAMED synthesis vendor publishes it can make: length, average and windowed GC, homopolymer runs, tandem repeats, long repeats and hairpin-forming inverted repeats. |
check_methylation_block | Whether the host's own methylation blocks the given enzymes ON THIS PLASMID, from REBASE's methylation-sensitivity tables localised onto your sites. |
check_rows | A QC gate over a TABLE: assert something about every row at once (every band inside a size window, no guide above an off-target score, at least three assays under a penalty). |
check_scorpion_stem | A Scorpion probe's two melting temperatures, side by side: the stem-loop's own hairpin and the duplex the loop makes with its target on the amplicon. |
check_value | A QC gate. Compares a wired value against a threshold and PASSES or FAILS the pipeline there — every node downstream of a failed gate is skipped, so a run stops at the first check that does not hold. |
classify_droplets | ddPCR droplet amplitudes to populations. For TWO targets, a four-way classification — NN, NP, PN, PP — under any of THREE published methods that answer different questions and none of which is a fallback for another. |
classify_grammar_part | Which Golden Braid / MoClo / Yeast ToolKit grammar, position and level the open plasmid represents (or null). |
codon_usage_analysis | Codon-usage analysis of an in-frame CDS: CAI / expression stats, GC, and every rare-codon occurrence for the chosen organism (pydna port), plus the two bias measures that need NO reference table — ENC (Wright 1990) and RCBS (Roymondal 2009), which are therefore computable for any organism. |
codon_usage_distance | How this region's codon usage compares with the record's OTHER genes (CUFS, Diament, Pinter & Tuller 2014). |
compare_antibodies | Several antibodies side by side: each record numbered by ANARCI, its heavy or its light variable domains aligned column by column by their numbering (a column is one scheme position, so nothing is re-aligned and an insertion is its own column), the CDR of every column under the chosen definition… |
compare_trees | Compare trees over the same taxa: the Robinson-Foulds distance between two of them, and the consensus of any number. |
convert_mass_moles | Convert a mass of a molecule to an amount in moles and a number of molecules, or an amount back to a mass. |
crispr_analyze_screen | Call HITS from a pooled CRISPR screen: per-guide read counts in, a gene-level Bayes factor and a precision/recall curve out. |
crispr_design_guides | Design and score CRISPR guides on the subject — on/off-target scores, QC flags, and cloning-enzyme conflicts. |
crispr_design_library | Turn the open record's annotated targets into an ORDERABLE sgRNA oligo pool: the best N guides per target, filtered at order time (Pol-III terminator, Graf inactive motif, cloning-enzyme site, minimum on-target score), each composed into the oligo a synthesiser makes — the vector's cloning… |
demultiplex_reads | Assign reads to the index each one came from, and say how many could NOT be assigned reliably — a hit further from a barcode than the set's guaranteed correction radius is not that barcode, and counting it as one is how a demultiplexing report hides a failed run. |
describe_tools | The full description of each named tool: what it computes, its models and options, and what it refuses. The listing on this endpoint carries only each description’s opening. |
design_barcodes | Design a set of NGS sample-index barcodes with a guaranteed minimum distance, and report what that set actually corrects — substitutions, or indels too (DNABarcodes). |
design_bisulfite_primers | Design BSP or MSP primers for a methylation assay, on the CONVERTED strands: after bisulfite treatment every unmethylated C reads as T, which is a different template from the one every other designer sees. |
design_codehop | Design CODEHOP hybrid oligos from a block of aligned PROTEIN - for homologues too diverged for nucleotide-level design to see at all. |
design_combinatorial_library | Design a combinatorial library in one step: SLOTS, each offering a bin of interchangeable parts, plus the CONSTANTS every member carries. |
design_degenerate_primers | Design degenerate primers from a multiple-sequence ALIGNMENT - the 'amplify every homologue in this family' question, which a single-template designer cannot answer because it only ever sees one sequence. |
design_expression_variants | The expression-design deliverable: several coding sequences for one protein, each variant following a different published strategy (maximise codon adaptation, match the host's codon usage, harmonise with the native host, or preserve the initiation region), each scored by an engine — CAI, GC, the… |
design_free_codes | Generate INDEL-correcting barcodes — FREE divergence codes (Hawkins et al., PNAS 2018) — by reserving each codeword's error sphere over the whole 4^k space, so the guarantee survives an insertion or deletion rather than only a substitution. |
design_fusion_site_primers | Design the PCR primers that ADD Type-IIS fusion sites to a part: enzyme site, spacer and the four-base overhang you chose, on a Tm-matched annealing footprint. |
design_gene_fragment_order | Write the sheet IDT's gene-fragment PLATE upload takes for one or more designed fragments: one worksheet per 96-well plate, wells in the template's own order, and the template's four columns (well, name, sequence, 5' phosphorylation). |
design_genetic_circuit | Design a genetic circuit that computes: give it a logic function and it synthesizes a NOR/NOT netlist, assigns real characterized repressor gates from a Cello UCF library, predicts the dynamic range between ON and OFF, and emits the construct's DNA. |
design_gibson_primers | Design the PCR primers that CREATE the terminal homology a Gibson/NEBuilder/In-Fusion assembly needs: a Tm-matched pair per fragment, each carrying the 5' overhang that fuses it to its neighbour in the order given (pydna assembly_fragments). |
design_hcr_probes | Design HCR v3.0 split-initiator probe pairs against the subject: tile its reverse complement into 52 nt windows, drop windows with C or G runs, a stable hairpin, G+C or RNA:DNA free energy outside their windows, or (given a bowtie2 alignment of the tiles) more than one genome hit, then pick… |
design_ish_probes | Design an in-situ hybridization probe against the subject: tile it into candidate oligos that meet a melting-temperature, G+C and composition specification, screen them for off-target binding against an alignment and for k-mers abundant in a reference, and gather the survivors into the set that… |
And 140 more tools.
In its maker's words
Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics
- Website
- jeanslabs.vercel.app/docs/api/mcp
- Publisher
- genmnz
- Listed from
- the official MCP Registry as
io.github.genmnz/jean - Version
- 2.0.0, updated 5 Nov 2026
- Kinds of work
- Health and science, Documents and files, Data and databases
Every call we made
| When | What happened | Time |
|---|---|---|
| Answered | 2590 ms | |
| Answered | 2911 ms | |
| Answered | 1203 ms |
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