What is a FASTA File and the FASTA Format?
Introduction
A FASTA file is a file written in FASTA format that describes nucleotide sequences or amino acid sequences. Extensions such as ".fasta", ".fa", ".fna", and ".fas" are used.
Lines that start with ">" contain the sequence name, ID, or description. The lines following this header, up until the next line starting with ">", contain a single sequence's information.
Line breaks can be freely inserted within a sequence. When line breaks are included, each line often contains about a few dozen characters. When searching for sequences in a standard text editor, keep in mind that line breaks within the sequence may cause searches to fail.
A file that includes not only nucleotide sequences but also their quality scores is called a FASTQ file. For a detailed explanation of FASTQ files, please see here.
Example of a FASTA File
Nucleic Acid Bases Used in FASTA Files
| Characters | Nucleic Acid Bases |
|---|---|
| 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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