FASTA-pro file format

Description

List of protein sequences are commonly stored in data files using the FASTA format. This simple ASCII text format looks like this:

>description line first protein
SEQUENCEPROTEINHERE
ANDHEREANDHEREAND
HEREAND
>description line second protein
SECONDPROTEINSEQUENCEHERE
...

This format has the advantage of being very easy to write and read. The description line is necessarily only one line long, which can limit its usefulness for recording detailed information.

A disadvantage of the FASTA format is that it is relatively slow to read with a computer. X! Tandem can also use a simple binary file version of an original FASTA file, which is about 6 times faster to read. The following illustration shows the structure of a FASTA-pro file:

size (bytes)	type	description
256	bytes	header
4	unsigned int	description line length N₁
N₁	ASCII bytes	description line (including string ending NULL character)
4	unsigned int	sequence length L₁
L₁	ASCII bytes	sequence (including string ending NULL character)
4	unsigned int	2nd description line length N₂
repeat length,description,length,sequence pattern