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Seq Regex Studio

Test regex on FASTA/FASTQ headers with live match highlighting, seqkit-style renaming, and CLI export—no account. Built-in AI agent assistant support.

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Key facts

Key facts about Seq Regex Studio
FactValue
InputFASTA headers (>), FASTQ @ lines, or plain header text — max 200 lines
ModesMatch & Filter; Find & Replace with $1, ${name}, {NR}
FlagsCase insensitive (i), multiline (m), dotall (s), invert (-v)
Templates11 presets: NCBI, UniProt, SRA, GISAID, Ensembl, Illumina, generic
Exportseqkit grep/replace, grep -P, Python snippet, CSV, clipboard
Runs in browserYes — client-side; optional API/MCP
AI assistantBuilt-in; fills pattern/input via manifest

What it does

Sequence header formats differ across NCBI, UniProt, SRA, and in-house pipelines, so a regex written for one dataset often fails silently on the next. Seq Regex Studio is a browser workspace for testing Perl-compatible regular expressions against up to 200 pasted FASTA or FASTQ headers before you run batch commands.

On the Regex workspace tab, choose Match & Filter or Find & Replace mode, type or paste a pattern, and see matched headers highlighted in green and non-matches in red as you type (150 ms debounce). Named capture groups populate a table; replacement mode supports `$1`, `${name}`, and `{NR}` record counters like seqkit replace. Toggle case-insensitive, multiline, dotall, and invert (-v) flags, load a mixed-format example dataset, copy seqkit grep/replace or grep -P commands, export CSV, or share a permalink URL.

The Template library tab lists searchable presets for NCBI RefSeq accessions, UniProt IDs, ENA/SRA run IDs, GISAID isolates, Ensembl genes, Illumina sample names, and pipe-delimited fields — each with a live preview on a realistic example header. The History tab recalls recent pattern-and-dataset sessions stored in your browser.

Why researchers use it

  • Preview regex matches on real headers before running seqkit grep on full FASTA files
  • See every non-matching record listed instead of silent empty output
  • Rename headers with capture groups and {NR} counters without writing scripts
  • Apply invert (-v) filtering to find outliers that break a pattern
  • Copy ready-to-run seqkit, grep -P, or Python snippets from current settings
  • Share exact pattern, flags, and sample data via URL hash permalinks

Best for

  • Filtering NCBI RefSeq or UniProt headers before downstream orthology pipelines
  • Renaming Illumina sample IDs with consistent capture-group templates
  • Debugging why seqkit grep returns fewer records than expected
  • Extracting accession fields from mixed legacy gi|pipe headers
  • Teaching wet-lab collaborators regex on familiar FASTA examples

When to use this vs alternatives

Use Seq Regex Studio when you need live visual feedback on biological sequence header regex before batch filtering or renaming. For computing sequence properties (MW, pI, GC%), use Sequence Property Calculator. For translating coding sequences or exploring codon tables, use Codon Code Lens. For production-scale filtering of multi-gigabyte FASTA files, export the CLI snippet and run seqkit or grep locally.

What makes it different

Command-line seqkit grep uses the RE2 engine, which rejects lookahead, lookbehind, and some Perl-style constructs that appear in real-world header cleanup recipes. Seq Regex Studio uses the browser's native JavaScript RegExp (ES2018+) for sub-millisecond live feedback on pasted samples, then exports equivalent CLI commands for your pipeline.

Unlike generic regex testers (Regex101), it understands FASTA/FASTQ header parsing, ships bioinformatics ID presets, surfaces named capture groups in a table, and targets seqkit replace parity — without uploading data to a server.

How to get started

  1. Open the Regex workspace tab and paste 5–20 FASTA headers (or click Load example).
  2. Choose Match & Filter or Find & Replace mode and enter a regex pattern — or pick a preset from Template library.
  3. Toggle flags (i, m, s, -v) and review green/red highlighted matches in the preview panel.
  4. In Replace mode, type a replacement using $1, ${name}, or {NR} and compare transformed headers inline.
  5. Review the match summary, named capture group table, and list of failed records.
  6. Copy CLI command, export CSV, or click Share link to save the session to History.

Frequently asked questions

Does this search nucleotide or protein sequences?
No. Seq Regex Studio applies regex only to sequence header/ID lines (text after > or @), not to residue sequences. Motif search on bases or amino acids belongs in a dedicated motif tool.
How does Find & Replace relate to seqkit replace?
Replacement mode evaluates your template with numbered ($1) and named (${name}) capture references plus a {NR} record counter, previewing the full transformed header text before you run seqkit replace -p PATTERN -r REPLACEMENT on a file.
What regex engine is used?
The workspace uses native JavaScript RegExp with ES2018+ named groups and lookaround support for instant client-side preview. Exported grep -P and Python snippets target PCRE-compatible syntax; seqkit commands use its RE2 engine (no lookaround).
What happens if my pattern is slow or invalid?
Invalid syntax shows a red border and error message with preview disabled. Patterns taking longer than 50 ms per header trigger a timeout warning suggesting simplification. Inputs beyond 200 header lines are trimmed with a banner.
Can I use an AI agent or MCP with Seq Regex Studio?
Yes. The workspace assistant reads your pattern and sample headers to help craft regex. External agents can call the same handler via [API & MCP](/tools/developers) using pepkio_seq-regex-studio.

Client source code & registry

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