TXT to FASTA converter

What is TXT to FASTA Converter?

The TXT to FASTA converter transforms plain text sequence data into properly formatted FASTA files, the standard format for representing nucleotide or protein sequences in bioinformatics.

FASTA format begins each sequence with a header line starting with ">", followed by the sequence data across one or more lines. This universal format is required by most sequence analysis tools, databases, and pipelines.

Converting sequences to FASTA format ensures compatibility with downstream analysis tools while providing standardized metadata through header lines. The converter handles various input formats including raw sequences, numbered sequences, and sequences with existing headers.

The tool automatically detects multiple sequences in a single text file and applies consistent formatting rules across all entries. We offer several other FASTA converters for different source formats, including CSV to FASTA, GenBank to FASTA, FASTQ to FASTA, and PDB to FASTA.

How does TXT to FASTA work?

The converter processes text input through several transformation stages to produce valid FASTA output.

First, it identifies individual sequences within the input text using configurable separation methods. The tool can automatically detect sequence boundaries, split on empty lines, or use custom delimiters to handle various input formats. This flexibility accommodates different data sources without requiring manual preprocessing.

After sequence identification, the converter generates appropriate header lines for each sequence. Headers can preserve existing labels from the input text, use sequential numbering (seq_1, seq_2), or intelligently extract identifiers from the surrounding text.

The smart extraction mode searches for common patterns like "protein_a" or numbered entries to create meaningful sequence names.

The final stage applies character-level transformations to ensure valid FASTA output. The tool removes whitespace, numbers, punctuation, and other non-sequence characters while converting the remaining letters to uppercase or lowercase as specified.

Line wrapping splits long sequences into multiple lines following the standard 80-character limit recommended by NCBI, though 60 characters and single-line output are also available. Sequence validation checks that all remaining characters are valid IUPAC codes for nucleotides or amino acids.

Input requirements & settings

The converter accepts plain text input either pasted directly or uploaded as a file. Supported file extensions include .txt, .fasta, .fa, .fas, .seq, and .dat, with a maximum file size of 50 MB.

Sequence detection

• Multi-sequences: Determines how the tool identifies separate sequences. Auto-detect analyzes text structure to find natural boundaries. Split on empty lines treats each block separated by blank lines as a distinct sequence. Custom separator lets you specify any delimiter string.

Header formatting

• Header format: Controls how sequence identifiers are generated. Preserve existing headers maintains any ">" lines already present. Sequential numbering options provide simple incrementing names. Custom prefix lets you define your own naming scheme. Extract from text (smart) attempts to identify meaningful names from surrounding text.

• Header extraction pattern: Refines smart extraction behavior. First word takes the initial word before each sequence. Line numbers searches for "1.", "2." patterns. Sequence identifiers looks for conventions like "seq1" or "protein_a".

Sequence formatting

• Line wrapping: The standard 80 characters per line follows NCBI recommendations. 60 characters is also common in many workflows. No wrapping outputs each sequence on a single line.

• Case format: Converts sequence letters to UPPERCASE, lowercase, or preserves original capitalization. Most databases expect uppercase sequences.

Character cleanup

• Character cleanup: Enables automatic removal of non-sequence characters. When enabled, you can selectively remove spaces, numbers, tabs, and punctuation.

• Remove invalid characters: Strips any letters that are not valid IUPAC codes, ensuring only valid nucleotide codes (A, C, G, T, U, N) or amino acid codes remain.

• Validate sequences: Performs a final check that all output characters are valid biological sequence codes.

• Add line numbers to headers: Includes original line numbers from the input file in FASTA headers, useful for tracking sequence sources.

Best practices

Order your input text with each sequence clearly separated to improve auto-detection accuracy. If working with multiple sequences, use consistent formatting throughout the input to ensure uniform processing.

For database submission or sharing with collaborators, use uppercase sequences with 80-character line wrapping to match NCBI standards. Enable all character cleanup options and validation to ensure your FASTA files contain only valid sequence data.

When converting sequences from publications or documents, the smart header extraction mode often produces more meaningful identifiers than simple numbering. Review the extracted headers to verify they captured the intended sequence names.

Common use cases

Researchers use this converter when transcribing sequences from PDF papers or supplementary materials that don't provide downloadable FASTA files. The tool handles common formatting issues like line numbers, spacing for readability, and descriptive text mixed with sequence data.

Laboratory workflows generate text files from sequencing instruments or analysis software that need conversion to FASTA for standard bioinformatics pipelines. The customizable cleanup options handle instrument-specific formatting without manual editing.

Educational contexts benefit from the converter when students need to format sequences from textbooks or assignments for hands-on analysis exercises. The validation features help catch transcription errors before submitting sequences to analysis tools.

Related tools

ProteinIQ offers several other format conversion tools that complement TXT to FASTA:

• CSV to FASTA — Convert tabular sequence data from spreadsheets
• GenBank to FASTA — Extract sequences from GenBank flat files
• FASTQ to FASTA — Convert sequencing reads by removing quality scores
• PDB to FASTA — Extract amino acid sequences from protein structures
• FASTA Splitter — Divide multi-sequence FASTA files into individual files
• FASTA to FASTQ — Add placeholder quality scores for pipeline compatibility