Mol Biology Tools

Estimates PCR primer melting temperatures and polymerase-specific annealing temperatures from sequence and buffer inputs, with per-pair QC for hairpins, dimers, and Tm balance. A browser calculator supports interactive single-pair and batch entry (up to 200 pairs) with method comparison and export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic for the API client is hosted remotely; sequences are transmitted for programmatic runs while the web interface performs calculations in the browser.

SeqBench is a browser-based workbench of 82 tools for molecular cloning, primer design and sequence analysis: nearest-neighbour melting temperature, oligo dimer and hairpin screening, in-silico PCR, site-directed mutagenesis, restriction mapping, Gibson, Golden Gate and restriction-ligation assembly simulation, plasmid annotation and backbone identification, CRISPR gRNA, HDR donor and base editing design, codon optimisation and CAI, pairwise and multiple alignment, RNA secondary structure, protein properties, Sanger ab1 traces, HGVS conversion and variant annotation. It verifies constructs as well as designing them: re-deriving an assembly from its stated parts and diffing it against the claimed product, aligning sequencing reads back onto a claimed reference, and scoring Golden Gate overhang sets against published ligation-fidelity data. Batch FASTA processing, multi-tool workflows, a conversational tool-calling interface (SeqBench-GPT), a REST API and an MCP server are included.

Derives cells per well and suspension pipette volumes for standard 6-, 12-, 24-, 48-, 96-, and 384-well plates from a hemocytometer stock count, trypan blue viability, and target seeding confluency, with QC flags for low viability and impractical transfers. A browser calculator supports interactive planning with cell-line presets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured plate tables and shareable run identifiers.

Plans geometric serial dilution series for molecular biology and biochemistry workflows, rounding transfer volumes to declared pipette ranges and optional 96- or 384-well plate layouts. A browser calculator supports interactive protocol design; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured step tables and shareable run identifiers.

This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.

Processes 96-well plate absorbance data through blank subtraction, regression fitting, and dilution correction to report sample concentrations with QC flags for BCA, Bradford, and ELISA workflows. A browser calculator supports interactive grid entry with CSV and PDF export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits plate layout and absorbance values and returns model comparison, per-sample concentrations, and shareable run identifiers.