7 bench tasks · 86 tools
Molecular biology tools
86 tools, all running in the browser on files that stay on this machine. They are one workbench rather than a set of utilities: each acts on the construct currently open, and hands its result to the next.
Cloning
10Cut, join and assemble constructs.
Run the BP and LR reactions on real sequences and see the entry and expression clones they produce.
Give the tool a vector and one or more inserts and it finds the terminal homology between them, orders the fragments, and builds the assembled…
Digest parts with a Type IIS enzyme, match the resulting four-base overhangs, and see the construct they assemble into.
Check that a part obeys the assembly syntax it claims, then assemble parts that do. Classification reads the real flanking overhangs and the Type IIS…
Join cut DNA and see what comes out before you set the reaction up. Give the tool molecules and their enzymes and it lists every fragment each digest…
Plan several assemblies at once and let them depend on each other: each level's constructs become parts for the next, so a promoter fused to a…
- Multi-site mutagenesisOpen the editor, then Tools, then Cloning.
Name the substitutions you want anywhere in a gene and get the mutagenic oligos for them, designed for the one-tube multi-site protocol.
Choose enzymes and see what they do to the sequence: every recognition site on both strands, the fragments a digest produces, and those fragments as…
- Site-saturation mutagenesisOpen the editor, then Tools, then Cloning.
Pick the residues you want to randomise and get the primer pairs that saturate them in one reaction.
Pick a coding sequence, state the change you want, and get the mutagenesis primers for it.
Amplify
16Primers, PCR and quantification.
- Amplification Curves → CqOpen the editor, then Tools, then Amplify.
Turn raw amplification curves into a Cq per reaction. Paste the cycle-by-cycle fluorescence your instrument exports, pick the sigmoid to fit (or let a…
Find the CpG islands in a sequence and design the primers that read methylation in one: a BSP pair that amplifies both alleles for sequencing, or the…
Design primers for a gene nobody has sequenced yet, using its relatives' proteins. A CODEHOP is one oligo with two halves: a short 3-prime core that…
Design one primer that amplifies a whole family. The input is an alignment rather than a single sequence, and every column of it gets the best…
- Digital PCROpen the editor, then Tools, then Amplify.
Turn partition counts into an absolute concentration. Paste the well table an instrument exports (positives and accepted partitions) and read copies…
- Droplet classificationOpen the editor, then Tools, then Amplify.
Sort a ddPCR well into its populations, and see how much of that sorting is the method rather than the data.
Turn a ddPCR amplitude export into a concentration you can defend. Give it the `_Amplitude.csv` files your droplet reader wrote — one per well, raw…
Design a complete loop-mediated isothermal amplification set against a region of an open sequence: the four core primers that recognise six regions of…
- Melt Curves → TmOpen the editor, then Tools, then Amplify.
Turn a melt (dissociation) curve into a melting temperature you can act on. Import the run your instrument exported, or paste the…
Compute the melting temperature of an oligo under conditions you state, rather than under conditions a tool assumed.
A multiplex fails on the pairs nobody checked. Build the pool and the template set, then screen every compatible pair against every template and read…
Collect the fragments you intend to join, from the open sequence, the current selection or pasted bases, and fuse the ones whose ends actually…
Check a primer pair against a template and get the product it would actually produce, or find that it produces none.
Design primers against a region of an open sequence and see the numbers that decide whether they will work: nearest-neighbour melting temperature…
The oligos you already own, kept with the constructs they belong to. Each primer carries its lifecycle state and its melting temperature, an order…
Design a qPCR assay against a region of an open sequence, then analyse the data that comes back from the instrument.
Design
12Engineer the sequence before you build it.
A GTF, GFF3 or BED lists features and their positions and carries no bases at all, so on its own there is nothing to look at.
Take a protein and get the DNA that would encode it, weighted by a real codon-usage table rather than by the first codon in a list.
Rewrite a coding sequence for expression in a chosen host while holding the constraints that matter: forbidden restriction sites, GC window,…
Work out what a CRISPR edit actually produced, from a pair of Sanger reads. Give it the unedited control trace, the edited trace and the guide, and it…
Find the guides in a target sequence and check where else they could cut. Guides are enumerated by PAM match on both strands, including guides that…
Generate a barcode set whose minimum distance is guaranteed rather than hoped for, inspect every barcode in it, and extend a set you are already…
Most design work tunes how strongly a gene is expressed. A genetic circuit is a different question: a construct that senses something, applies a logic…
An in-situ hybridization experiment images one RNA or one locus inside a cell by hybridizing many short oligos along it.
A sequence that arrived as bare bases can be scanned for the features it carries: promoters, operators, origins of replication, resistance genes,…
Find out how many replicates a planned experiment needs to detect the effect you care about, or what power the design you can afford really has.
Work on the translation-initiation side of an expression construct: read the strength of an existing ribosome binding site, design a 5-prime UTR…
Put a table of candidates in, say which columns should be high and which low, and see which ones no other candidate beats on every count at once.
Analyze
31Inspect what a sequence is and how it behaves.
Find the signal peptides and transmembrane segments in reviewed human UniProt that a sequence predictor scores unlike the experimentally confirmed…
Number an antibody the way the literature does. Paste or select a protein, and every antibody or T-cell-receptor variable domain in it is found, typed…
- Assay decay: does a published assay still match current genomes, and is the mismatch at the 3′ endOpen →
Take an assay somebody published years ago and ask whether its primers and probes still match the sequences circulating now.
Ask one question and have it answered by the database that actually owns the answer.
BLAST where the sequence already is. Pick a target from the open construct rather than pasting bases into a form, run it against the database you…
The local aligner stays the default. This is for the moment a result has to be defensible: run the same sequences through the aligner the field cites…
Score every coding sequence of a genome against the genome's own codon usage and find the genes whose choice among synonymous codons that average does…
Read the codon composition of a coding sequence against a host: which codons are rare in that host, what the codon adaptation index comes to, and how…
A codon optimisation is only as good as the usage table behind it. Build one from a real CDS corpus, either whole-genome or from the highly expressed…
- TableOpen the editor, then Tools, then Analyze.
Open a CSV, TSV or Parquet as a real tab on the stage and read it as a table: sort by a column, resize it, filter to the rows that mention a thing.
Everything drawn on the map, read as a table instead. Each tab carries its live count, each row selects its span on the map, and features, parts and…
Put two sequences on two axes and see what they share. A dot plot is the fastest way to see structure that a single alignment score hides: a tandem…
Ask which loci of a multi-locus alignment have a different history from the rest. For every locus, the test counts how many extra parsimony steps it…
Register a hypothesis and the test that will answer it before any evidence exists, attach the runs that test it, and decide across every hypothesis…
- ImageOpen the editor, then Tools, then Analyze.
Open the `.tif` nothing else will. A 16-bit micrograph straight off a microscope looks black in most viewers because its pixels use a sixteenth of the…
- StructureOpen the editor, then Tools, then Analyze.
Keep the structure with the construct. Which chains this entry holds, which residues were actually resolved, what is bound in the site and how many…
- Mass spectrometry: peptide masses, b ladders, isotopes, spectrum scoring, q-values, protein inferenceOpen →
Weigh a peptide, generate its fragment ladder and isotope envelope, score a spectrum against it, estimate the false discovery rate of a search, and…
- NumPy ArrayOpen the editor, then Tools, then Analyze.
Open a NumPy array in the browser and see what is actually in it: the values, the shape and the dtype, without starting Python.
- PDFOpen the editor, then Tools, then Analyze.
Keep the paper with the data. A protocol, a supplementary file or the study your constructs came from opens as a real tab beside the sequences it…
Turn an alignment into a tree and judge how well the data supports it. Four inference methods are available, bootstrap support is computed per branch,…
Cut a protein with any of forty-nine proteases and chemicals and read the peptides it would produce, with their masses and m/z, without leaving the…
Read the physicochemical properties of a protein the way ExPASy ProtParam does, without leaving the editor or pasting a sequence into a form.
Take a CDS from the construct you have open, scan it against the InterPro member databases, and put the domains back on the map at DNA coordinates.
- Reagent audit: does each annotated CDS code for what the map says, and are its cryptic promoters, splice sites and repeats worse than chanceOpen →
Check that each annotated coding sequence of a vector map codes for what the map says it does.
Test whether the genes used to normalise expression are steadier across human tissues than genes of the same abundance.
The enzyme list, scoped to the sequence you have open: every enzyme carries how many times it cuts this construct, Type IIS enzymes are flagged as…
Ask which restriction sites a set of genomes carries far less often, or far more often, than chance predicts.
- MoleculeOpen the editor, then Tools, then Analyze.
Keep the reagent with the construct. The antibiotic your resistance gene protects against, the inducer you added, the dye in your master mix, as a…
Test a hypothesis that a gene drives a phenotype, such as "RAC2 regulates IL-2 production", the way POPPER does.
Test every gene alignment against the species tree and find the genes whose own sites reject it.
Render fragments as bands on an agarose gel before running the real one. Lanes accept the output of a restriction digest or a linearised plasmid, the…
Sequencing
11Reads, alignments and verification.
Open a sorted, indexed BAM (or a SAM, which needs no index) and look at a locus: the coverage over the window and the reads beneath it, drawn from the…
Open a capillary fragment run and turn its peaks into lengths. A fragment run is the other document the ABIF format carries: dye channels and a size…
Put sequencing reads where they came from on a reference. Illumina reads (single or paired), Nanopore and PacBio long reads, and assembled contigs are…
Align a set of sequences and read the result as an alignment you can navigate: per-sequence identity, column conservation, and the scores that…
Read a cohort's genotypes population by population: allele frequencies, heterozygosity and exact Hardy–Weinberg tests per site, Fst between…
Find the genes whose expression differs between conditions from raw RNA-seq read counts with the model DESeq2 fits, then ask which gene sets those…
- ChromatogramOpen the editor, then Tools, then Sequencing.
Open a Sanger trace in the browser and work on it: inspect the four dye channels, read per-base Phred confidence, correct a base call, trim the noisy…
Open a Sanger trace in the browser and work on it: inspect the four dye channels, read per-base Phred confidence, correct a base call, trim the noisy…
Answer the question a sequencing result is meant to answer: does this clone match the intended construct.
- Variant CallsOpen the editor, then Tools, then Sequencing.
Open a VCF and read it as variant calls rather than as text: a table with typed INFO fields, per-sample genotypes, and htslib’s own allele…
Find sequence that came from the vector rather than from the insert. A construct, a selected region or a set of reads is screened against NCBI UniVec…
Record
5Capture what you did and hand it on.
The same operations the panels run, wired into a graph. Connections are typed, so an output can only be joined to an input that accepts it, and the…
Recover how a construct was made. A SnapGene file or a QUEEN-authored GenBank that carries a build history is read into the lineage of operations…
The notebook sits in the same workbench as the constructs, so an entry can name the plasmid it was run on and that name is a link.
Read a file in one format and write it in another without a round trip through a server.
Read a file in one format and write it in another without a round trip through a server.
Documents
1The editors the tools act on.
- Plasmid EditorOpen the editor to use it.
Open a plasmid and work on it in the view that suits the task: the circular map for the whole construct, the linear map for a region, the sequence…