FASTA format
Bioinformatics · Genomics · Molecular Biology
Say it: FAST-ay FOR-mat
FASTA format is a plain-text format for DNA, RNA or protein sequences in which each record starts with a header line beginning with > followed by the sequence.
Also: FASTA, FASTA file
Definition
What is FASTA format?
FASTA format is the simplest and most common way to store and exchange biological sequences. Each record begins with a single description line, often called the header or defline, that starts with a greater-than sign (>) and gives an identifier and sometimes a short description. The lines below it hold the sequence itself, written in one-letter codes for nucleotides or amino acids. A file can hold one sequence or many, one record after another.
Because it is plain text, a FASTA file opens in any text editor and is read by almost every bioinformatics program. Sequences use the standard IUPAC letters, so N can mark an unknown base, X an unknown amino acid and a dash a gap. NCBI recommends keeping lines under 80 characters and leaving no blank lines inside the data. The format holds no quality scores, so raw sequencing reads are often stored in the related FASTQ format instead.
The name comes from the FASTA sequence-comparison programs written by William Pearson and David Lipman in the 1980s. Students meet it when downloading a gene from GenBank or pasting a query into BLAST.
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Related
Terms that go with it
- BLASTBLAST is a widely used program that searches databases for DNA or protein sequences similar to a query and ranks the matches by statistical significance.
- Sequence alignmentSequence alignment is a way of lining up two or more DNA, RNA or protein sequences so that matching positions share a column, showing how similar they are.
- BioinformaticsBioinformatics is the science of using computers to gather, store, analyze and share biological data, especially DNA, RNA and protein sequences.
- DNADNA is the double-stranded molecule that carries the genetic instructions of nearly all living things, written in a code of four bases: A, T, C and G.
- Next-generation sequencingNext-generation sequencing (NGS) is a set of high-throughput methods that read the sequences of millions of short DNA fragments in parallel.
- GenomeA genome is the complete set of DNA in an organism or cell, including all of its genes and the stretches of DNA between them.
Sources
Checked against
Written for biofideX in plain words, after checking these references:
- NCBI BLAST: Query input and database selection
- DOE Joint Genome Institute MycoCosm: FASTA format
- FASTA program package documentation, version 2.0 (W. R. Pearson, University of Virginia)
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