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FASTA Molecular Weight Calculator

Batch FASTA MW, pI, and GC% for DNA, RNA, and protein—CSV export, no account. Built-in AI agent assistant support.

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Key facts

Key facts about FASTA Molecular Weight Calculator
FactValue
InputsMulti-FASTA paste, drag-drop, or file upload (.fa, .fasta, .txt)
Max batch sizeUp to 500 sequences; 5 MB file limit
OutputsMW, length, GC%, pI, ε260, ε280 (native and denatured), GRAVY, instability index per row
OptionsAverage or monoisotopic mass; linear or circular topology; single- or double-strand (ε260 for DNA)
Concentration panelPer-row mass (pg–g) + volume µL, or A260/A280 + pathlength → molar and mass concentration, copy/µL
ExportCSV (comma or semicolon), copy table (TSV), per-row copy, permalink
Additional tabsDilution (simple or serial C₁V₁); Ligation (insert mass from lengths and molar ratio)
Session historyLast 10 runs stored in browser
Runs in browserYes — no install
Account requiredNo

What it does

ExPASy ProtParam forces one protein at a time with no export, and DNA or RNA calculators live on separate sites—so mixed construct lists mean tab-switching and hand-copying MW, pI, and GC% into Excel. The FASTA molecular weight calculator accepts mixed multi-FASTA input and returns a complete property table in one browser session, updated live as you paste.

Paste or upload into FASTA sequences; each row is auto-classified as DNA, RNA, or protein with a per-row Type override. Toggle Mass (Avg or Mono), Topology (linear or circular), and Strand (single or double for ε260 on DNA). The table shows length, MW, GC%, pI, extinction coefficients, GRAVY, and instability index; ambiguous bases trigger per-row warnings without blocking valid rows.

Click a row for the Concentration panel—enter mass and volume µL, or A260/A280 and pathlength, for molarity and copy number from that row's MW and ε. Export CSV, Copy table, or Permalink. Dilution and Ligation tabs handle C₁V₁ and cloning insert mass in the same workspace.

Why researchers use it

  • Analyze hundreds of sequences without rerunning ProtParam one-by-one
  • Skip switching between separate DNA, RNA, and protein calculators
  • Export a complete property table instead of hand-copying results
  • Convert OD readings to molarity using each row MW and ε
  • Share exact inputs with collaborators via permalink
  • Flag ambiguous bases and type mismatches before ordering oligos

Best for

  • Proteomics or construct lists needing batch MW and pI
  • Oligo and primer molecular weight checks before synthesis
  • IVT template and coding-sequence comparisons across molecule types
  • Cloning insert mass planning on the Ligation tab
  • Synthetic biology part libraries with mixed DNA and protein entries
  • Converting nanodrop A260 or A280 readings per sequence

When to use this vs alternatives

Choose this tool when mixed DNA, RNA, and protein FASTA must become one sortable, exportable property table in a single session. Use the Molecular Mass Converter when you already have OD, mass, or molar values and need unit conversion or batch NanoDrop paste—not full sequence property analysis. Use the Serial Dilution Planner when dilution planning needs pipette rounding or 96/384-well plate maps; the built-in Dilution tab covers simple C₁V₁ and lightweight serial steps only. ExPASy ProtParam remains a trusted single-protein check when you need the classic reference for one sequence.

What makes it different

Most alternatives handle one molecule type or one sequence at a time, and few combine property calculation with exportable tables and integrated concentration math. ExPASy ProtParam is the gold-standard single-protein reference but accepts one sequence per run with no CSV. SMS2 and similar DNA calculators cover nucleic acids only with weak export. Biopython ProtParam batches programmatically but requires Python.

This browser FASTA molecular weight calculator unifies mixed DNA, RNA, and protein batch analysis with live results, Avg/Mono toggle, CSV export, row-level concentration math, and permalink sharing—no install or account. Researchers switch when construct panels outgrow one-at-a-time ProtParam, mixed FASTA forces multiple calculator tabs, or lab records need a downloadable table instead of copied plain text.

How to get started

  1. Open the workspace and stay on the Sequence tab.
  2. Paste into FASTA sequences, drag-drop a file, or click Browse; try Load example… to preview output.
  3. Set Mass (Avg or Mono), Topology, and Strand for your nucleic acid convention.
  4. Review the live results table; override Type per row if needed; click a row for the Concentration panel.
  5. Click Export CSV or Copy table; click Permalink to copy a shareable link.
  6. Open Dilution for C₁V₁ or serial dilution, or Ligation for required insert mass.

Frequently asked questions

How do I calculate molecular weight from a FASTA sequence?
Paste or upload your sequence in FASTA format—the header line starts with > followed by an optional name, then the sequence on following lines. The calculator sums residue masses for DNA, RNA, or protein using your selected average or monoisotopic mass setting. For nucleic acids, choose linear or circular topology; MW updates live as you edit. Results appear in the table with length, MW in Da or kDa, and related properties for that molecule type.
Can I analyze DNA, RNA, and protein in one batch?
Yes. Paste a multi-FASTA file with mixed sequence types; each header block is analyzed independently. The tool auto-detects DNA, RNA, or protein from composition and shows the assigned Type per row. Override the dropdown when you know the intended molecule class differs from auto-detection. Up to 500 sequences per session are supported.
What is the difference between average and monoisotopic mass?
Average mass uses mean isotopic weights per residue—common for bulk biochemical work and vendor datasheets. Monoisotopic mass uses the most abundant isotope per atom—standard for mass spectrometry and precise peptide mapping. Toggle Mass between Avg and Mono; all rows recalculate instantly. Protein pI, GRAVY, and instability index are unchanged by this toggle; MW and concentration outputs reflect your choice.
How do I convert A260 or A280 to concentration?
Click a valid row in the results table to open the Concentration panel. Under From OD, select A260 (nucleic acids) or A280 (proteins), enter your measured OD and pathlength in cm (default 1 cm). The tool applies the row computed extinction coefficient to return molarity in your chosen unit plus mass concentration. Alternatively, enter Mass and Volume µL under From mass when you know the amount dissolved.
Why does my oligo MW differ from IDT or OligoCalc?
This calculator reports nucleic acid MW in 5′ monophosphate form—the convention used for restriction-cut DNA and many academic tables. Synthetic oligos from vendors often quote 5′/3′ hydroxyl form, which is about 79 Da lower per strand. If your oligo MW is consistently ~79 Da below IDT/OligoCalc, the difference is likely this terminal chemistry convention—not a calculation error.
How does this compare to ExPASy ProtParam?
ProtParam remains the widely cited reference for single-protein MW, pI, extinction coefficient, GRAVY, and instability index. It accepts one sequence per submission, offers no CSV export, and covers protein only. This calculator implements comparable protein properties plus nucleic acid MW, GC%, and ε260 in one batch table with export, concentration conversion, and mixed FASTA support.

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