There are some pitfalls to the traditional FASTA file format. ProteomeCommons supports the efforts of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI) to improve the format and the way it is used. This page describes the standardized FASTA format.

FASTA

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Note: not all issues have been worked out. The parts of this page that are still in question are shown in red text.
Among the other items that haven't been worked out:

• FASTA file extension (.fasta, .seqa, or something else?)
• Do we always need DBPrefix in all entries, even if only one database?
• Taxonomy information in protein headers: NCBI_TaxID > latin name > common name (mapping changes regularly)
• Splicing variants: separate entries or annotations?
• Processed sequences: separate entries or annotation? (removal of precursor peptide, active chain, …)
• CV of database names
• CV of internal terms

HUPO Standardized FASTA Format

A source file that includes: A file header-block with information about the included database(s) All lines in the block start with the '#' character One header term from the list below per line Individual protein (polypeptide) entries One header line in the form that starts with the '>' character The sequence

File Header

Terms for the header	Description	Value
#\DbComponent=	Count increment	Integer
#\Name=	Name of the database	CV from database provider (UniprotKnowledgeBase)
#\PrimaryIdentifierType=	Identifier to be used as prefix for individual protein entries	CV
#\Decoy=	Is it a decoy database	?: true/false or description
#\Version=	Databse version, according to the database provider	According to the database provider
#\ReleaseDate=	The date of the source database
#\NumberOfEntries=	Number of entries	Integer
#\Sequence_type=	Sequence type	DNA, AA, RNA, EST, etc.

Individual Protein Entries

Description of the individual entry header line	Example
Header starts with >, followed by primary AC, preceded with the Database prefix (useful if more than one DB are concatenated). Mandatory field.	>sp_ac|P000761
Description of all non-sequence information \term=value (terms are controlled vocabulary descriptors)	\ID=ALBU_HUMAN
The order of the additional fields is not important
Value can be a list. The elements of the list are represented as (value_1)(value_2)	\ALTERNATE_AC=(P00786)(Q22222)
Value can be imbedded into " " if needed	\DE="Human serum albumin"
'|' can be used as separator for all individual fields	\MODRES=(1|Acetyl)
Ctrl-A as separator for multi-header entries ? (NCBInr usecase)	(NCBInr usecase)

Header Field Term	Definition	Format
ALT_AC	Alternative AC
ID	SwissProt_ID
DE	protein description
ALT_DE	alternative description
NCBITAXID	NCBI taxonomy identifier (9606)	integer
TAX_LATIN	taxonomy in latin name (Homo sapiens)
TAX_COM	taxonomy in common name format (human)
MODRES	modified residue (PTM)	(position|modification) (PSI_MOD)
VARIANT	residue mutation	(Position|original residue|final residue)