All capabilities
Every tool and panel in the workbench, what runs it, and where to find it.
86 tools and 50 panels. "Reached by" is the menu path the editor declares, or the dialogs that open a panel with no menu entry.
Cloning
| Tool | Reached by | Page |
|---|---|---|
| Restriction Digest | Tools → Cloning | open |
| Ligation | Tools → Cloning | open |
| Gibson Assembly (experimental) | Tools → Cloning | open |
| Golden Gate Assembly (experimental) | Tools → Cloning | open |
| Grammar Assembly (experimental) | Tools → Cloning | open |
| Assembly Plan (experimental) | Tools → Cloning | open |
| Recombination Cloning | Tools → Cloning | open |
| Site-Directed Mutagenesis (experimental) | Tools → Cloning | open |
| Site-saturation mutagenesis | Tools → Cloning | open |
| Multi-site mutagenesis | Tools → Cloning | open |
Amplify
| Tool | Reached by | Page |
|---|---|---|
| Primer Designer (experimental) | Tools → Amplify | open |
| LAMP primer set (experimental) | Tools → Amplify | open |
| Bisulfite methylation primers (experimental) | Tools → Amplify | open |
| Degenerate primers from an alignment (experimental) | Tools → Amplify | open |
| CODEHOP hybrid primers from a protein alignment (experimental) | Tools → Amplify | open |
| Primer Library (experimental) | Tools → Amplify | open |
| PCR Simulation (experimental) | Tools → Amplify | open |
| Fusion PCR (experimental) | Tools → Amplify | open |
| Multiplex PCR (experimental) | Tools → Amplify | open |
| qPCR Design | Tools → Amplify | open |
| Digital PCR | Tools → Amplify | open |
| Amplification Curves → Cq | Tools → Amplify | open |
| Melt Curves → Tm | Tools → Amplify | open |
| Droplet gating → concentration | Tools → Amplify | open |
| Droplet classification | Tools → Amplify | open |
| Melting Temperature | Tools → Amplify | open |
Design
| Tool | Reached by | Page |
|---|---|---|
| Codon Optimization (experimental) | Tools → Design | open |
| Back-translate: protein → DNA, codon-usage weighted or degenerate | Tools → Design | open |
| CRISPR Guide Design (experimental) | Tools → Design | open |
| Genetic Circuit | Tools → Design | open |
| In-Situ Probes | Tools → Design | open |
| CRISPR Edit Inference | Tools → Design | open |
| RBS & Operon Design (experimental) | Tools → Design | open |
| Barcode & Index Design | Tools → Design | open |
| Auto-Annotate (experimental) | Tools → Design | open |
| Apply features from a file | Tools → Design | open |
| Power and sample size: replicates needed to detect an effect, or the power a design has | Tools → Design | open |
| Trade-offs: which candidates in a table are not beaten on every objective at once | Tools → Design | open |
Analyze
| Tool | Reached by | Page |
|---|---|---|
| Properties | View → Properties | open |
| BLAST Search | Tools → Analyze | open |
| Search Databases | Tools → Analyze | open |
| EMBL-EBI Services | Tools → Analyze | open |
| Protein Domains | Tools → Analyze | open |
| Protein Analysis | Tools → Analyze | open |
| Protease Digest | Tools → Analyze | open |
| Antibody Numbering | Tools → Analyze | open |
| Mass spectrometry: peptide masses, b ladders, isotopes, spectrum scoring, q-values, protein inference | Tools → Analyze | open |
| Codon Usage Analysis (experimental) | Tools → Analyze | open |
| Site avoidance: restriction sites a genome avoids or favors | Tools → Analyze | open |
| Codon outliers: genes whose codon usage departs from their own genome | Tools → Analyze | open |
| Tree incongruence: genes whose own alignment rejects the species tree | Tools → Analyze | open |
| Reference stability: reference genes against genes of their own abundance | Tools → Analyze | open |
| Annotation contradictions: UniProt features a predictor scores unlike confirmed ones | Tools → Analyze | open |
| Hypothesis ledger: pre-register a hypothesis, attach runs, decide with e-BH | Tools → Analyze | open |
| Reagent audit: does each annotated CDS code for what the map says, and are its cryptic promoters, splice sites and repeats worse than chance | Tools → Analyze | open |
| Assay decay: does a published assay still match current genomes, and is the mismatch at the 3′ end | Tools → Analyze | open |
| Gene incongruence: which loci of a multi-locus alignment have a different history | Tools → Analyze | open |
| Target validation: test "gene G drives phenotype P" against gene-level evidence tables | Tools → Analyze | open |
| Codon Tables (experimental) | Tools → Analyze | open |
| Enzyme Collections (experimental) | Tools → Analyze | open |
| Virtual Gel Bench (experimental) | Tools → Analyze | open |
| Phylogenetics | Tools → Analyze | open |
| Dot Plot | Tools → Analyze | open |
| Table | Tools → Analyze | open |
| NumPy Array | Tools → Analyze | open |
| Structure | Tools → Analyze | open |
| Tools → Analyze | open | |
| Molecule | Tools → Analyze | open |
| Image | Tools → Analyze | open |
Sequencing
| Tool | Reached by | Page |
|---|---|---|
| Chromatogram | Tools → Sequencing | open |
| Map reads to a reference | Tools → Sequencing | open |
| Fragment analysis | Tools → Sequencing | open |
| Alignment | Tools → Sequencing | open |
| Variant Calls | Tools → Sequencing | open |
| Population genetics: allele frequencies, Hardy–Weinberg, Fst, linkage disequilibrium | Tools → Sequencing | open |
| RNA-seq: differential expression with DESeq2, over-represented gene sets, gene set enrichment | Tools → Sequencing | open |
| Multiple Sequence Alignment | Tools → Sequencing | open |
| Compare Traces to Reference | Tools → Sequencing | open |
| Sequencing Verification (experimental) | Tools → Sequencing | open |
| Screen for vector contamination | Tools → Sequencing | open |
Record
| Tool | Reached by | Page |
|---|---|---|
| Lab Notebook (experimental) | Tools → Record | open |
| Workflow Builder (experimental) | Tools → Record | open |
| History (experimental) | Tools → Record | open |
| Export | File → Export… | open |
| Export Image | File → Export Image… | open |
Documents
| Tool | Reached by | Page |
|---|---|---|
| Plasmid Editor | None | open |
Panels
| Tool | Reached by | Page |
|---|---|---|
| Edit annotation | AddOrEditFeatureDialog, AddOrEditPartDialog, AddOrEditPrimerDialog | open |
| Enzyme | AdditionalCutsiteInfoDialog | open |
| Insert sequence | SequenceInsertDialog | open |
| Merge features | MergeFeaturesDialog | open |
| Manage enzymes | EnzymesDialog | open |
| Dot plot | None | open |
| Dot plot grid | None | open |
| Melt curve | None | open |
| Amplification curves | None | open |
| Population genetics | None | open |
| RNA-seq | None | open |
| Site avoidance heat map | None | open |
| Protein coverage | None | open |
| Reference-gene stability | None | open |
| Digital PCR | None | open |
| Codon usage matrix | None | open |
| Pairwise distance distribution | None | open |
| Nearest-neighbor distances | None | open |
| GC content distribution | None | open |
| Base composition per cycle | None | open |
| Pairwise distance grid | None | open |
| Per-cycle channel occupancy | None | open |
| Grammar assembly plan | None | open |
| Gibson assembly plan | None | open |
| Assembly plan build order | None | open |
| Golden Gate assembly plan | None | open |
| Guide track | None | open |
| Primer binding track | None | open |
| Hydropathy profile | None | open |
| Charge vs pH | None | open |
| Amino-acid composition | None | open |
| Hydrophobic moment | None | open |
| Optimization profiles | None | open |
| Digest gel | None | open |
| Virtual gel | None | open |
| Initiation-window fold | None | open |
| Antibody domain map | None | open |
| Electropherogram | None | open |
| Circuit netlist | None | open |
| Circuit transfer functions | None | open |
| Circuit construct | None | open |
| Construction graph | None | open |
| Protocol | None | open |
| Read Quality Profile | None | open |
| Read Alignment | None | open |
| Raw Signal | None | open |
| Verify vs Reference | None | open |
| Chromosomal microarray | None | open |
| Variant calls | None | open |
| Small molecule | None | open |
Check a run's read quality, and settle its encoding
The route: open the reads → read the per-cycle curve → decide where to trim → and before you believe any of it, settle which quality encoding the file is written in.
Restriction Digest
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 bands on a virtual gel.