What Is FASTA

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∟What Is FASTA

This section provides a quick introduction of FASTA, FastA, a universal file format or representing either a nucleotide sequence or a peptide (protein) sequence, in which base pairs or amino acids are represented using single-letter codes.

What Is FASTA? - FASTA, or FastA, is a file format for representing either a nucleotide sequence or a peptide (protein) sequence, in which base pairs or amino acids are represented using single-letter codes.

FASTA file format was introduced by the FASTA software, which is a DNA and protein sequence search and alignment tool developed by by David J. Lipman and William R. Pearson in 1985.

FASTA is now become a near universal standard in the field of bioinformatics. And it is supported by every bioinformatic tools.

A FASTA file may contain multiple sequences. Each sequence starts with one line to provide an identifier and other information with a prefix of ">" as the first characher of the line. After the identifier line, the sequence data is provided in one or more lines.

As an example, the smallest protein sequence, Trp-Cage, can be written in a FASTA format file as:

>1L2Y_1|Chain A|TC5b|null
NLYIQWLKDGGPSSGRPPPS

Here is another example of FASTA files with 2 protein sequences:

>gi|186681228|ref|YP_001864424.1| phycoerythrobilin:ferredoxin oxidoreductase
MNSERSDVTLYQPFLDYAIAYMRSRLDLEPYPIPTGFESNSAVVGKGKNQEEVVTTSYAFQTAKLRQIRA
AHVQGGNSLQVLNFVIFPHLNYDLPFFGADLVTLPGGHLIALDMQPLFRDDSAYQAKYTEPILPIFHAHQ
QHLSWGGDFPEEAQPFFSPAFLWTRPQETAVVETQVFAAFKDYLKAYLDFVEQAEAVTDSQNLVAIKQAQ
LRYLRYRAEKDPARGMFKRFYGAEWTEEYIHGFLFDLERKLTVVK
>1L2Y_1|Chain A|TC5b|null
NLYIQWLKDGGPSSGRPPPS