DNA Sequence Utilities

Sequence transforms, file-format conversion between FASTA, FASTQ, GenBank, EMBL, Clustal, PHYLIP and NEXUS, feature and CDS extraction, and FASTQ read quality control.

A growing toolbox of one-click operations on sequence files. Paste or upload your data, pick an operation below, and the result appears in the Result tab ready to copy or download.

Operations work on plain sequence (FASTA, tab-delimited "name sequence", or a single bare sequence) and clean every record to IUPAC letters first. File formats, annotations & reads works on the file as written — it reads FASTA, FASTQ, GenBank, EMBL, Clustal, PHYLIP and NEXUS, detects which one you pasted, and keeps headers, gaps, quality strings and feature tables intact.

Retrieve from NCBI by accession — chromosomes (NC_), mRNA (NM_), RefSeq contigs
Upload a local sequence file — FASTA, FASTQ, GenBank, EMBL, Clustal, PHYLIP, NEXUS or plain text
Operations
Strand transforms
Case
Methylation
Reformat & report
Clustering
Shared k-mers %

More transforms will be added here over time — each is independent, so this list will keep growing.

File formats, annotations & reads

Unlike the operations above, everything in this card reads the file exactly as written — headers, gaps, quality strings and feature tables are preserved rather than stripped. The input format is detected automatically; override it only when the guess is wrong.

Convert between formats
Output options
Features & CDS — GenBank / EMBL input

Spliced join(…) and complement(…) locations are assembled correctly, and a translation is checked against the record's own /translation.

Sequencing reads — FASTQ input

Phred+33 and Phred+64 encodings are detected automatically. The report covers per-position quality and base composition, read-length distribution, duplication and an adapter screen.

Need details? Supported file formats, every operation and its limits are documented in Help: Sequence Utilities
Exporting results: use Download for a file in the right format, or click inside the result area → Ctrl+ACtrl+C → paste into Excel.