FASTA Format: File Structure & Examples
Introduction
A FASTA file is a text file in FASTA format used to store nucleotide or amino acid sequences. Common file extensions include ".fasta", ".fa", ".fna", and ".fas".
Lines beginning with ">" serve as headers, containing the sequence name, ID, or description. Everything from the header line to the next ">" line (or end of file) constitutes a single sequence entry.
Line breaks can appear anywhere within a sequence. When present, lines are typically wrapped to a fixed width of around 60-80 characters. Be aware that if you search for a sequence in a standard text editor, line breaks within the sequence may prevent matches.
A file format that stores both nucleotide sequences and their quality scores is called FASTQ. For more details on the FASTQ format, see here.
Example of a FASTA File
Nucleic Acid Bases Used in FASTA Files
| Character | Nucleic Acid Base |
|---|---|
| G | Guanine |
| C | Cytosine |
| A | Adenine |
| T | Thymine |
| M | Adenine or Cytosine |
| R | Adenine or Guanine |
| W | Adenine or Thymine |
| S | Cytosine or Guanine |
| Y | Cytosine or Thymine |
| K | Guanine or Thymine |
| V | Adenine or Cytosine or Guanine |
| H | Adenine or Cytosine or Thymine |
| D | Adenine or Guanine or Thymine |
| B | Cytosine or Guanine or Thymine |
| N | Adenine or Cytosine or Guanine or Thymine |
| - | Gap |
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About the Author
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A research support company specializing in bioinformatics.
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