FASTA Converter - Oligonucleotide Sequence Format Converter
Convert oligonucleotide sequences between FASTA, CSV, TSV, and plain text formats for vendor ordering (IDT, Twist Bioscience, GenScript). Features automatic format detection, IUPAC nucleotide validation, reverse complement for primer design, deduplication, and batch processing. Process thousands of oligo pool sequences instantly with privacy-first browser-based conversion.
Input & Options
Results
No results yet
Select format and convert your sequences
FASTA Converter Guide - Oligonucleotide Format Conversion
Oligonucleotide Format Conversion for Vendor Ordering
Converting oligonucleotide sequences between formats is essential for modern molecular biology workflows. This FASTA converter streamlines vendor ordering by converting between FASTA, CSV, and TSV formats required by oligonucleotide synthesis vendors including IDT (Integrated DNA Technologies), Twist Bioscience, and GenScript. The tool ensures format compatibility while maintaining sequence integrity through IUPAC nucleotide validation and automated quality control.
All oligonucleotide processing occurs client-side in your browser using optimized algorithms. Zero data transmission to external servers ensures complete privacy for proprietary primer sequences, oligo pools, and custom library designs. This architecture makes the tool ideal for handling confidential research data and commercial oligonucleotide projects.
Vendor Format Requirements (2025 Current Specifications)
IDT (Integrated DNA Technologies)
IDT accepts CSV/Excel format with columns: Name, Sequence, Scale, Purification. Use CSV output with uppercase conversion and sequence validation enabled. Compatible with IDT's bulk ordering system and custom oligo pool synthesis (capacity varies by synthesis method: standard pools, high-throughput pools, or custom configurations).
Tip: IDT also accepts plain text format (one sequence per line) for simple orders via their online ordering interface.
Twist Bioscience
Twist requires CSV format with Name and Sequence columns for oligo pool orders. Enable deduplication and validation to ensure library quality before upload. Standard oligo pools support 10,000-12,000 sequences depending on complexity and length (50-350 bases per oligo).
Note: Twist's high-fidelity pools may have different capacity limits. Consult Twist specifications for your specific application.
GenScript
GenScript accepts Excel-compatible CSV or TSV formats with flexible column arrangements. Standard oligo pools accommodate up to 12,400 sequences per current specifications. Use TSV for sequences containing special characters or international annotations. All IUPAC nucleotide codes supported.
⚠️ Important Disclaimer: Vendor specifications, column requirements, and capacity limits are subject to change. Information above reflects November 2025 current offerings. Always verify format requirements, pricing, and capacity limits directly with your chosen vendor before submitting large orders. Contact vendor technical support for the most up-to-date specifications and custom synthesis options.
Supported Formats - Side-by-Side Comparison
| Format | Example (Same Data) | Use Cases |
|---|---|---|
| FASTA | >primer_F1 Forward primer 1 ATCGATCGTAGCTAGC >primer_F2 Forward primer 2 GCTAGCTAGCATCGAT | NCBI/EMBL submission, BLAST searches, sequence alignment tools, archival storage |
| CSV | ID,Sequence,Description primer_F1,ATCGATCGTAGCTAGC,Forward primer 1 primer_F2,GCTAGCTAGCATCGAT,Forward primer 2 | Vendor ordering (IDT, Twist), Excel analysis, metadata annotation, collaborative sharing |
| TSV | ID Sequence Description primer_F1 ATCGATCGTAGCTAGC Forward primer 1 primer_F2 GCTAGCTAGCATCGAT Forward primer 2 | Command-line tools, bioinformatics pipelines, international characters, special symbols |
| Plain Text | ATCGATCGTAGCTAGC GCTAGCTAGCATCGAT | Batch processing, script input, minimal formatting tools (Note: IDs are lost) |
FASTA Format Specifications
FASTA is the de facto standard in bioinformatics, recognized by virtually all sequence analysis tools and databases. Header lines begin with > followed by sequence ID and optional description. Sequences typically wrap at 60-80 characters per line (per NCBI guidelines), though single-line sequences are also valid.
NCBI Submission Requirements: Sequence IDs must be unique, contain no spaces (use underscores), and be ≤50 characters. Required for GenBank submissions as of 2025.
CSV (Comma-Separated Values)
CSV format organizes sequences in a tabular structure with columns separated by commas. This format is particularly useful for spreadsheet applications like Excel or Google Sheets, allowing researchers to add metadata, annotations, or analysis results alongside sequences.
ID,Sequence,Description,GC_Content seq1,ATCGATCGATCG,Example sequence 1,50.0 seq2,GCTAGCTAGCTA,Example sequence 2,50.0
CSV format is essential for vendor ordering systems, quality control spreadsheets, and collaborative data sharing where multiple researchers need to review and annotate sequences.
TSV (Tab-Separated Values)
TSV format uses tabs instead of commas as delimiters, making it more robust for sequences that may contain commas in descriptions or metadata. This format is preferred when sequences include special characters or when working with international character sets.
TSV is commonly used in high-throughput sequencing pipelines and is the preferred format for many command-line bioinformatics tools.
Plain Text Format
Plain text format contains one sequence per line with no headers or metadata. This is the simplest format and is ideal for batch processing, script-based workflows, or when sequence identifiers are not required.
Plain text is perfect for quick conversions, bulk sequence processing, or when preparing sequences for tools that require minimal formatting.
Step-by-Step Usage Guide
Step 1: Prepare Your Input
Copy and paste your sequences directly into the input field, or use the"Upload File" button to load sequences from a file. The tool supports files up to 10MB, which typically accommodates tens of thousands of sequences. Supported file extensions include .fasta, .fa, .csv, .tsv, and .txt.
Tip: For large datasets, uploading a file is faster than pasting. The tool automatically detects the format, but you can manually specify it if needed.
Step 2: Select Output Format
Choose your desired output format from the dropdown menu. Consider your downstream application: use FASTA for database submissions or alignment tools, CSV for spreadsheet analysis, TSV for command-line tools, or plain text for simple batch processing.
Tip: If you're unsure, FASTA is the most universally compatible format and can be easily converted again later if needed.
Step 3: Configure Processing Options
Enable relevant processing options based on your needs:
- Validate Sequences: Removes sequences containing invalid nucleotide characters. Essential for ensuring data quality.
- Remove Duplicates: Eliminates identical sequences, keeping only the first occurrence. Useful for cleaning merged libraries.
- Reverse Complement: Converts all sequences to their reverse complement. Critical for primer design workflows.
- Convert to Uppercase: Standardizes sequence case for consistent downstream processing.
Step 4: Optional ID Modification
Add prefixes or suffixes to sequence IDs for better organization. For example, adding "Primer_" as a prefix will rename sequences to"Primer_seq1","Primer_seq2", etc. This is particularly useful when preparing sequences for vendor ordering or organizing multiple libraries.
Step 5: Convert and Review
Click"Convert Format" (or press Ctrl+Enter / Cmd+Enter) to process your sequences. The tool displays conversion statistics including original count, final count, invalid sequences removed, and duplicates eliminated. Review the output preview, then copy to clipboard or download as a file.
Real-World Calculation Examples
Example 1: FASTA to CSV for Vendor Ordering
Scenario: You have 50 primer sequences in FASTA format and need to submit them to a vendor that requires CSV format.
Input: FASTA file with 50 sequences
Settings: Output format: CSV, Validate sequences: Enabled, Convert to uppercase: Enabled, Add prefix:"Primer_"
Result: CSV file with columns: ID, Sequence, Description. All sequences validated, converted to uppercase, and renamed with"Primer_" prefix. Ready for direct import into vendor ordering system.
Example 2: Cleaning and Deduplicating a Library
Scenario: You've merged multiple sequence libraries and need to remove duplicates and invalid sequences.
Input: CSV file with 10,000 sequences (estimated 200 duplicates, 50 invalid)
Settings: Output format: FASTA, Validate sequences: Enabled, Remove duplicates: Enabled
Result: FASTA file with 9,750 sequences. Statistics show: 10,000 original, 9,750 final, 50 invalid removed, 200 duplicates removed. Library is now clean and ready for analysis.
Example 3: Reverse Complement Calculation for PCR Primers (Step-by-Step)
Scenario: Design reverse primers from forward primer sequences for PCR amplification.
Input (Plain Text Format):
ATCGATCGTAGCTAGC GCTAGCATGCATGCTA CGATCGWSKMRYBDHV
Settings: Output format: FASTA, Reverse complement: Enabled, Convert to uppercase: Enabled, Add prefix:"RC_"
Calculation Process (Sequence 1: ATCGATCGTAGCTAGC):
- Original: 5'-ATCGATCGTAGCTAGC-3'
- Step 1 - Reverse: GCGATCGATGCTAGCTA (reading 3'→5')
- Step 2 - Complement: GCTAGCTAGCATCGAT (A→T, T→A, C→G, G→C)
- Final reverse complement: 5'-GCTAGCTAGCATCGAT-3'
Ambiguity Code Example (Sequence 3: CGATCGWSKMRYBDHV):
- W(A/T)→W, S(G/C)→S, K(G/T)→M(A/C), M→K, R(A/G)→Y(C/T), Y→R
- B(CGT)→V(ACG), D(AGT)→H(ACT), H→D, V→B
- Result: VHDBYRKMSWGATCG
Output (FASTA Format with RC_ prefix):
>RC_seq1 GCTAGCTAGCATCGAT >RC_seq2 TAGCATGCATGCTAGC >RC_seq3 VHDBYRKMSWGATCG
Next Steps: Use Tm Calculator to validate that forward and reverse primer pairs have similar melting temperatures (within 3-5°C), then check secondary structures for primer dimers.
Understanding Conversion Results
After conversion, the tool provides comprehensive statistics to help you understand what happened to your sequences:
Key Metrics Explained
- Original Count: Total number of sequences detected in the input file. This includes all sequences before any processing.
- Final Count: Number of sequences in the output after validation and deduplication. This is the count of sequences that will be in your converted file.
- Invalid Sequences: Sequences containing characters that are not valid nucleotide codes (ATCGURYMKSWBDHVN). These sequences are excluded from the output to ensure data quality.
- Duplicates Removed: Number of duplicate sequences eliminated when deduplication is enabled. Only the first occurrence of each unique sequence is kept.
Important Notes
- If validation warnings appear, review your input sequences for non-standard characters
- Large output files may be truncated in the preview - always download the full file for complete results
- Sequence IDs are preserved when converting between formats that support headers (FASTA, CSV, TSV)
- When converting to plain text, sequence IDs are lost - use FASTA format if IDs are important
Common Issues and Solutions
❌ Issue: Sequences with Spaces or Line Breaks
Problem: Input like"ATCG ATCG" or sequences with internal line breaks cause validation errors.
Solution: The converter automatically removes spaces and line breaks within sequences. For FASTA format, ensure each sequence is either on a single line OR properly wrapped with no blank lines between sequence continuation lines.
❌ Issue: Mixed Case or Lowercase Sequences
Problem: Vendor systems often require uppercase sequences, but input contains mixed case.
Solution: Enable"Convert to Uppercase" option before conversion. This standardizes all sequences to uppercase (ATCG) as required by IDT, Twist, and most vendor ordering systems.
❌ Issue: CSV Column Headers Don't Match Vendor Requirements
Problem: Output CSV has"ID, Sequence, Description" but vendor requires"Name, Sequence, Scale".
Solution: After conversion, open CSV in Excel and rename column headers to match vendor specifications. IDT typically requires: Name, Sequence, Scale, Purification. Twist requires: Name, Sequence. Add any missing columns (Scale, Purification) manually.
❌ Issue: Special Characters in Sequence IDs
Problem: IDs like"primer#1" or"seq (copy)" contain symbols that cause CSV parsing errors.
Solution: Use underscores instead of spaces/symbols (e.g.,"primer_1","seq_copy"). For NCBI/GenBank submission, IDs must contain only alphanumeric characters, underscores, hyphens, and periods.
❌ Issue: Excel Opening CSV with Encoding Problems
Problem: CSV file shows garbled characters or weird symbols when opened in Excel.
Solution: This converter outputs UTF-8 encoded CSV files. In Excel (Windows), use "Data → Get Data → From File → From Text/CSV" and select UTF-8 encoding. On Mac, Excel should auto-detect UTF-8. For maximum compatibility, stick to standard ASCII characters (A-Z, 0-9, underscore).
IUPAC Nucleotide Validation and Technical Standards
This oligonucleotide format converter implements strict IUPAC (International Union of Pure and Applied Chemistry) nucleotide code validation, ensuring compatibility with major sequence databases (NCBI GenBank, EMBL, DDBJ) and vendor ordering systems. All conversion algorithms adhere to standardized bioinformatics formats established through decades of molecular biology research and software development.
Complete IUPAC Nucleotide Code Reference (IUBMB Standard)
| Code | Represents | Mnemonic | Complement |
|---|---|---|---|
| A | Adenine | - | T |
| T | Thymine (DNA) | - | A |
| C | Cytosine | - | G |
| G | Guanine | - | C |
| U | Uracil (RNA) | - | A |
| R | A or G | puRine | Y |
| Y | C or T | pYrimidine | R |
| S | G or C | Strong (3 H-bonds) | S |
| W | A or T | Weak (2 H-bonds) | W |
| K | G or T | Keto group | M |
| M | A or C | aMino group | K |
| B | C or G or T | not A | V |
| D | A or G or T | not C | H |
| H | A or C or T | not G | D |
| V | A or C or G | not T | B |
| N | Any nucleotide (A/T/C/G) | aNy | N |
Reference: IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN). All codes validated against NCBI GenBank standards as of 2025.
Reverse Complement Algorithm: The tool implements complete Watson-Crick base pairing rules for accurate reverse complement generation. Standard bases: A↔T, C↔G, U↔A (RNA). Ambiguity code transformations follow IUPAC complementarity: R↔Y (purine↔pyrimidine), K↔M (keto↔amino), S→S (strong bonds preserved), W→W (weak bonds preserved), B↔V (not-A ↔ not-T), D↔H (not-C ↔ not-G), N→N (any remains any).
The algorithm executes in two sequential steps: (1) Reverse: sequence order is reversed from 3'→5' orientation to 5'→3' (e.g., ATCG becomes GCTA), then (2) Complement: each base is replaced with its Watson-Crick complement (GCTA becomes CGAT). Final result for input ATCG is reverse complement CGAT. This is essential for PCR primer design where reverse primers must anneal to the antisense strand in antiparallel orientation.
Deduplication Method: The case-insensitive deduplication algorithm normalizes all sequences to uppercase before comparison, ensuring that"ATCG","atcg", and"AtCg" are recognized as identical. This is essential for oligo pool library quality control where duplicates may be introduced during data merging from multiple sources or synthesis rounds. The algorithm preserves the first occurrence while removing subsequent duplicates, maintaining original sequence IDs and metadata.
Format Detection: Advanced pattern recognition analyzes file structure to automatically identify FASTA (header lines starting with >), CSV (comma-delimited with optional headers), TSV (tab-delimited), or plain text (one sequence per line). This reduces user error and streamlines batch processing workflows for large oligonucleotide libraries.
Advanced Features
- ✓Auto-Detection: Advanced pattern recognition automatically identifies input format, reducing user error
- ✓IUPAC Validation: Comprehensive validation against all standard nucleotide codes ensures data quality
- ✓Case-Insensitive Deduplication: Identifies duplicates regardless of sequence case
- ✓Privacy-First Architecture: All processing occurs client-side - no data transmission to servers
- ✓Batch Processing: Handles thousands of sequences efficiently using optimized algorithms
Oligonucleotide Format Conversion Workflows
- Vendor Ordering: Convert FASTA to CSV for IDT, Twist Bioscience, and GenScript ordering systems. Combine with Molecular Weight Calculator to calculate oligo amounts for resuspension.
- PCR Primer Design: Generate reverse complement sequences for primer pairs. Validate Tm with Tm Calculator and check secondary structures using Secondary Structure Predictor.
- Oligo Pool Library QC: Deduplicate and validate oligo pools before synthesis. Use Batch Sequence QC for comprehensive quality control and GC Content Analyzer for distribution analysis.
- Database Submission: Convert vendor CSV files to FASTA for NCBI GenBank or EMBL submission. Ensure IUPAC compliance with automated validation.
- Collaborative Analysis: Export sequences to Excel-compatible CSV for team annotation and sharing across research groups.
Complete Oligo Design Pipeline:
1. Design sequences → 2. Convert format (this tool) → 3. Calculate Tm and GC content → 4. Check secondary structures → 5. Calculate molecular weight → 6. Quality control → 7. Submit to vendor
Frequently Asked Questions
The FASTA converter supports conversion between FASTA, CSV, TSV, and plain text formats - all standard formats used in oligonucleotide synthesis and molecular biology workflows. Automatic format detection identifies input structure, or you can manually specify the format. All oligonucleotide processing occurs client-side in your browser with zero server transmission, ensuring complete privacy for proprietary sequences. Handles files up to 10MB (typically 50,000+ oligonucleotides).
Need more help? Visit our complete FAQ or check the User Guide for detailed documentation on file formats and conversion workflows.
Related Tools
Batch Sequence QC
Comprehensive quality control for oligo pools - validate IUPAC codes, GC content, length distribution, and complexity metrics for thousands of sequences
GC Content Analyzer
Analyze GC% distribution across oligonucleotide libraries - critical for synthesis success and PCR primer design validation
Tm Calculator
Calculate oligonucleotide melting temperature with multiple methods (Nearest Neighbor, Wallace, GC-based) for PCR primer pair validation
Secondary Structure Predictor
Identify hairpins, self-dimers, and hetero-dimers in primers and oligos - essential for avoiding PCR amplification failures
Molecular Weight Calculator
Calculate oligonucleotide molecular weight, extinction coefficient, and resuspension volumes for concentration preparation
Vendor Format Adapter
Generate vendor-specific order files for IDT, Twist Bioscience, GenScript with proper formatting and metadata columns