SeqBench
https://bio.tools/seqbench-onlineSeqBench 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.
Sourced from
- bio.tools — seqbench-online
Related resources
Molecular Biology Tools is a free browser-based collection of molecular biology utilities for routine sequence analysis, primer design, Sanger sequencing primer planning, cloning setup, and wet-lab calculations. The site includes tools for PCR primer design, Sanger primer design and primer walking, primer binding checks, restriction site analysis, reverse complement generation, ORF and protein translation, codon optimization, ligation calculations, molarity calculations, dilution calculations, and multi-solute solution recipe preparation. The tools run in the browser and are intended for quick experimental planning, without requiring logins or uploading sequences to the server.
Browser-based viewer that maps sequencing reads onto one short reference — an amplicon, gene or plasmid. Reads open as Sanger AB1/ABIF, SCF, FASTA, FASTQ or a SAM somebody else already mapped (gzipped files are unpacked in place); the reference as FASTA, GenBank or a read. Both read orientations are tried automatically. The pileup reports per-position depth, where reads disagree with the target, and the consensus — phred-weighted for capillary reads, which keep their chromatogram under the letters. An optional protein lane translates target and consensus side by side. Reads are placed by minimap2 compiled to WebAssembly, or by the built-in aligner. One read or the whole alignment saves as FASTA. Runs entirely in the browser — files are never uploaded.
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.
Toolkit for processing sequences in FASTA/Q formats.
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.