FASTA and FASTQ

File Format
Name	FASTA and FASTQ
Ontology	Electronic File Formats Scientific Data formats FASTA and FASTQ
Extension(s)	.fasta, .fas, .fa, .seq, .fsa, .fna, .ffn, .faa, .mpfa, .frn, .fastq

FASTA and FASTQ are text-based formats for representing nucleotide (DNA or RNA) or peptide sequences, used in biology. The FASTA format is a simple representation of the elements of the sequences using letters (the standard C, G, T, and A for DNA nucleotides, and other letters for special uses, as well as a set of letters for peptides in amino acids), while FASTQ also encodes quality scores for the data.

File extensions

A number of extensions are used, and they are not always completely standardized.

• .fasta, .fas, .fa, .seq, .fsa: Generic FASTA
• .fna: FASTA nucleic acids
• .ffn: FASTA nucleotide coding regions for a genome
• .faa FASTA amino acids
• .mpfa: FASTA amino acides in multiple proteins
• .frn: FASTA non-coding RNA
• .fastq: FASTQ

Files may also be distributed in compressed forms, adding second extensions such as .fastq.gz.

Links

• Wikipedia: FASTA
• Wikipedia: FASTQ
• What is FASTA format?
• Single letter codes for nucleotides
• Processing Illumina data: FASTQ format
• Format FASTQ sequences and barcode data
• FASTA format converter
• Bio::SeqIO (Perl) (more info) (connected with Bio::Seq)
• SeqIO (Python) (connected with Seq) (more info)