What is FASTA and how is it used?

FASTA is among the most popular formats for storing biological sequence data. Here is what it is and how it is used.

What is FASTA?

The FASTA format is a text-based file format for storing protein and nucleic acid sequences. FASTA files commonly have the .fasta or .fa file extensions.

A FASTA file can contain one or more sequences. A sequence "block" in FASTA starts with a single-line description. The description line always begins with a greater-than character (>).

The sequence description line is immediately followed by the lines of sequence data. The residues in the sequence are represented using single-letter codes.

Here is an example of one protein sequence in the FASTA format:

Bottom line

Whether you perform sequence analysis on a daily basis or only occasionally run BLAST, it is important that you are familiar with the FASTA format and can easily open FASTA file and navigate their contents. To open and view FASTA files, you can use the web-based Sequence Alignment Viewer which is free to use and does not require downloading or installation.

See also

• Sequence Logo Generator - Create sequence logos from FASTA alignments.
• WebLogo in the browser - Bringing WebLogo to the browser + demo of a pure client side sequence logo maker.
• Sequence Alignment Viewer - Open FASTA files in the browser.
• GenBank to FASTA - Convert GenBank flat files to FASTA format.
• ABI to FASTA - Convert AB1 files (Applied Biosystems/ABI trace files) to FASTA format.
• FASTA Editor - A FASTA editor for creating and editing FASTA files.
• FASTA Parse Tree Viewer - Visualize the parse tree of FASTA files.
• FASTQ to FASTA Converter - Convert FASTQ files to FASTA format.
• PDB to FASTA - Extract protein/nucleotide sequences from PDB files.
• BLAST WASM - Compiling the BLAST sequence search/alignment tool to WASM.
• DESeq2 in the browser - Running DESeq2 in the browser.
• Genome Browser - Explore the human genome.
• Phylogenetic Tree Editor - An online visual editor for phylogenetic trees (WIP).
• Phylogenetic Tree Builder - Reconstruct phylogenetic trees from protein or DNA/RNA sequence alignments.
• Plasmid Map Generator - A tool to generate plasmid maps from GenBank files.
• WikiPathways: A Wikipedia for biological pathways - An overview of the collaboratively edited structured pathway encyclopedia.
• The RDF model of the Gene Ontology, demystified - An outline of the structure of the Gene Ontology RDF graph and ways to query it.
• The ambitious challenge of finishing the human genome - Generating a complete human genome sequence, chromosome by chromosome.
• Scalable genomic alignment with Progressive Cactus - How progressive alignment makes it possible to efficiently align hundreds to thousands of large genomes.
• Awesome bioinformatics - A curated list of awesome resources on bioinformatics.
• NCBI Taxonomy Browser - A simple tool for viewing the NCBI taxonomy tree.
• FASTQ Editor - A FASTQ editor for creating and editing FASTQ files.
• Newick Editor - An online editor for phylogenetic trees in the Newick format.
• Newick Parse Tree Viewer - View the parse trees of Newick strings.
• PDB Editor - Edit PDB files online.
• Bioinformatics Crossword - A daily crossword puzzle for bioinformatics terms.
• Bioinformatics pronunciation guide - A pronunciation guide for bioinformatics terms.