FASTAFormat

FASTAFormat refers to the FASTA format, a widely used text-based standard for representing nucleotide or protein sequences in bioinformatics. In FASTA files, each sequence entry begins with a header line that starts with the greater-than symbol (>), followed by an identifier and optional description. The lines that follow contain the sequence data, typically wrapped for readability, using standard one-letter codes for nucleotides (A, C, G, T, U, N and other IUPAC ambiguity codes) or amino acids.

Structure and conventions

A FASTA entry consists of a single header line and one or more lines of sequence data. The header provides a unique identifier and may include descriptive metadata such as organism, gene name, or accession numbers. The actual sequence is a string of letters without spaces, usually uppercase, though many tools accept lowercase as well. Multiple entries can appear in one file, each starting with its own header line. There is no formal schema for the header beyond convention, so fields are often separated by spaces, pipes, or other delimiters.

Common usage

FASTA is a de facto standard for sequence storage and exchange. It is compatible with many database submissions, sequence searching tools (such as BLAST), and multiple sequence alignment programs. Its simple structure makes it easy to parse programmatically, but it provides minimal metadata beyond what is included in the header.

History and variants

The format emerged with early sequence analysis tools in the 1980s and has remained widely adopted due to its simplicity and readability. While primarily described as FASTA, some references use the term FASTA format interchangeably. There are no formalized metadata fields within the format; users often encode additional information in the header text.

Example

>seq1 Homo sapiens example

ATGCGTACGTTAGC

GCTACGATCGATCG