What is the FASTA file format?
The .fasta format belongs to the category of bioinformatics data files. Contents of .fasta files include sequences of genetic data - they can contain information about the structure of DNA and RNA, but also about protein structures. The content is organized in a layout specific to this standard. One of its characteristic features is a > header line (called a defline), in which an identifier and descriptive annotations can also be recorded. One or more lines of raw sequence letters follow each header, using IUPAC nucleotide or amino-acid codes.
.fasta files can store a large number of sequences in a single file, which is why multi-.fasta files are often used as reference databases. All this information is used by specialized programs for genetic analyses. Thanks to the .fasta format, DNA comparative tests can be performed, as well as studies on the evolution of genetic structures.
Because .fasta stores only the identifier and raw sequence - without quality scores or rich annotations - complementary formats are often used alongside it: .fastq files add per-base quality scores for sequencing reads, while GenBank files carry full feature annotations. The format was developed by William R. Pearson and David J. Lipman for their FASTA sequence-comparison program and has since become the baseline plain-text standard for sharing biological sequences across tools and databases worldwide.
Common variant extensions include .fa, .fna (nucleotide sequences), .faa (amino-acid sequences), and .ffn (coding sequences).
Security & safety
RISK: LOWA FASTA file is plain-text sequence data with no executable content, so it is very low risk to open. The realistic cautions are practical, not security: whole-genome FASTA can be hundreds of MB to many GB and may freeze a basic text editor (use a streaming viewer like AliView or command-line seqkit/samtools faidx), and watch for malformed headers or mixed line endings that break downstream tools. Get reference sequences from authoritative sources (NCBI, Ensembl, UniProt) to ensure data integrity.
Format details
in a nutshellPrograms that open FASTA files
Windows5 apps
Jalview
Free Open the .fasta to view/edit and align sequences with a rich alignment viewer (Java, free).
UGENE
Open-source Open the .fasta in this free integrated bioinformatics suite to view, align and analyze.
SnapGene / SnapGene Viewer
Freemium Open the .fasta to view sequences and (with SnapGene) design cloning; the free Viewer reads FASTA.
Notepad++ (plain text)
Open-source Open small FASTA files as text to read or edit headers/sequences directly. 
macOS3 apps
AliView
Open-source Fast, free alignment viewer/editor - open the .fasta to view and edit large alignments. 
Linux2 apps
EMBOSS / Bioconda command-line tools
Open-source Use seqret/infoseq (EMBOSS) or seqkit/samtools to inspect, index and convert FASTA on the command line. Technical details
deep spec| Format type | Plain-text biological sequence format; one or more records per file |
| File encoding | ASCII / UTF-8 plain text; no binary data |
| Record header marker | ">" (greater-than, 0x3E) at byte offset 0 of each header line - the only pseudo-magic identifier |
| Header (defline) structure | ">identifier description" per NCBI defline convention, widely followed by databases and tools |
| Sequence alphabet | IUPAC nucleotide codes (A, C, G, T, U, N, ambiguity codes) for DNA/RNA; single-letter amino-acid codes for protein |
| Multi-record support | Unlimited records per file (multi-FASTA); a single file can serve as a full reference database |
| Sequence line wrapping | Typically 60-80 characters per line; wrapping is cosmetic - conformant tools reassemble the sequence ignoring line breaks |
| Quality scores | Not supported; raw sequence only - per-base quality data requires the FASTQ format instead |
| Annotation support | Identifier and free-text description in the header only; no feature or coordinate annotations (use GenBank/.gb or GFF3 for those) |
| Compression | None native; commonly distributed gzip-compressed as .fasta.gz or .fa.gz |
| MIME type | text/x-fasta (also seen: text/plain, application/x-fasta) |
| Typical file size | A few KB for a single gene or protein, up to tens of GB for whole-genome or reference databases |
| Variant extensions | .fa (generic), .fna (nucleotide), .faa (amino acid), .ffn (coding sequences), .frn (non-coding RNA) |
| In-file integrity check | None; reference releases are typically accompanied by external .md5 checksum files |
| Platform usage | Cross-platform; dominant in Linux/HPC bioinformatics pipelines, with broad support on Windows and macOS tools |
| Interoperability | Accepted as input/output by virtually all sequence-analysis tools: BLAST, BWA, STAR, Bowtie2, EMBOSS, Biopython, and others |
| Released | 1985 (FASTP/FASTA sequence-comparison program; format formalized 1988) |
| Latest version | De facto standard; no formal versioned spec (NCBI defline conventions widely followed) |
| Open standard | Yes · royalty-free |
| Specification | www.ncbi.nlm.nih.gov |
FASTA conversions
Community Q&A
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