fasta

FASTA is a text-based format for representing nucleotide or protein sequences. It was introduced in 1985 by William R. Pearson and David J. Lipman as part of the FASTA software suite used for sequence comparison. A FASTA file consists of one or more records. Each record starts with a header line beginning with a greater-than sign (>), followed by an identifier and optional description. The header line is used to identify the sequence. Subsequent lines contain the sequence letters (DNA, RNA, or protein) and may be wrapped to any width; whitespace is ignored when parsing.

Characters used in sequences follow standard alphabets: nucleotides use A, C, G, T (or U for RNA) and ambiguity codes such as N; amino acids use the 20 standard letters plus occasional ambiguity codes. Lowercase and uppercase are usually treated equivalently, though many tools prefer uppercase.

FASTA is widely used in public sequence databases such as GenBank, EMBL, and DDBJ, and as a common input format for alignment, search, and annotation tools (for example BLAST, Clustal, HMMER). There are variants for different applications; for example, multi-FASTA files contain multiple records in one file, each starting with a header line. Common file extensions include .fasta, .fa, .fna (nucleotide), and .faa (protein).

Limitations include the lack of a strict standard for metadata outside the header and the fact that the header contents are free-text. Despite this, FASTA remains a simple, widely supported format for representing biological sequences.

Example:

>seq1 Homo sapiens sample 1

ATGCGTACGTTAGC

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