The FASTA format is a simple, text-based standard used in bioinformatics to store and exchange biological sequences. It represents either nucleotide sequences (DNA or RNA) or amino acid sequences (proteins). Originating in the 1980s, its straightforward nature established it as a foundational method for handling raw sequence data, allowing researchers and software to consistently interpret these biological building blocks.
The Core Structure
Every FASTA entry has two distinct parts: a mandatory description line and the sequence data. The description line, or header, must be the first line of the entry and begins with the greater-than symbol (>). This symbol acts as a unique marker, signaling to software that the following text is metadata, not sequence information.
The text immediately following the “>” uniquely identifies the sequence and often includes a brief description. This entire description line must be contained on a single line without breaks. In files containing multiple sequences, each new entry starts with a new header line beginning with the “>” symbol.
The sequence data begins on the line immediately following the description line. DNA and RNA sequences use single-letter codes (A, T, C, G, or U), often including N for ambiguous bases. Protein sequences are represented using the standard one-letter codes for the 20 amino acids.
The sequence is often broken across multiple lines for human readability, though this wrapping is not required. The format ignores any spaces, tabs, or line breaks within the sequence data section. Bioinformatics software automatically concatenates all sequence lines into one continuous string for analysis.
Why This Format Matters
The enduring relevance of the FASTA format stems from its simplicity, which offers significant functional advantages. Since the format is purely text-based, it is inherently human-readable, allowing scientists to easily view and edit sequences using any basic text editor. This plain text structure eliminates compatibility issues, enabling seamless data transfer across different operating systems.
The greater-than symbol acts as a header delimiter specifically designed for efficient machine parsing. Software can rapidly scan for the “>” character to delineate where one sequence ends and the next begins. This clear separation of descriptive information from raw data is fundamental to how high-throughput tools process massive datasets quickly.
This minimalistic design contrasts with more intricate formats containing additional layers of information, such as quality scores or complex annotation fields. FASTA ensures that sequence storage and processing are computationally efficient, which is important when dealing with millions of sequences in large-scale genomic projects. It has become the de facto standard, ensuring interoperability across bioinformatics tools.
Common Applications
The primary use of the FASTA format is its function as the standard output for major public sequence repositories worldwide. Databases like the National Center for Biotechnology Information (NCBI) GenBank and the UniProt protein knowledge base allow users to download sequences in FASTA format. This makes it the most common way researchers share and acquire sequence data for their studies.
Sequence Searching and Alignment
FASTA files are the required input for nearly all sequence alignment and search tools. For instance, a researcher uses a FASTA-formatted query sequence to search for similar sequences within a vast database using tools like the Basic Local Alignment Search Tool (BLAST). Similarly, for comparing three or more sequences, a multi-FASTA file is fed into multiple sequence alignment programs such as Clustal or MUSCLE.
Genomics and Scripting
In large-scale genomics, the format plays a central role in both genome assembly and annotation projects. Newly sequenced DNA fragments are often stored in a FASTA-like format before being pieced together to form complete contiguous sequences, or contigs. The final reference genome sequence is then often represented as a single or multi-FASTA file, serving as the basis for all subsequent analysis. Additionally, its ease of handling makes it the preferred format for researchers writing custom scripts in programming languages like Python or R.