FASTA format
From Wikipedia, the free encyclopedia
In bioinformatics, FASTA format (a.k.a. Pearson format) is a text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences.
The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages like Python and Perl.
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[edit] Format
A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (both are optional). There should be no space between the ">" and the first letter of the identifier. It is recommended that all lines of text be shorter than 80 characters. The sequence ends if another line starting with a ">" appears; this indicates the start of another sequence. A simple example of one sequence in FASTA format:
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY
[edit] Format converters
FASTA files can be batch converted to or from MultiFASTA format using tools some of which are available as freeware. Tools are also available for batch conversion from chromatogram formats (ABI/SCF) to FASTA.
[edit] Header line
The header line, which begins with '>', gives a name and/or a unique identifier for the sequence, and often lots of other information too. Many different sequence databases use standardized headers, which helps when automatically extracting information from the header. The header line may contain more than one header, separated by a ^A (Control-A) character (as in [1]).
In the original Pearson FASTA format, one or more comments, distinguished by a semi-colon at the beginning of the line, may occur after the header. Most databases and bioinformatics applications do not recognize these comments and follow the NCBI FASTA specification. An example of a multiple sequence FASTA file follows:
>SEQUENCE_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
[edit] Sequence representation
After the header line and comments, one or more lines may follow describing the sequence: each line of a sequence should have fewer than 80 characters. Sequences may be protein sequences or nucleic acid sequences, and they can contain gaps or alignment characters (see sequence alignment). Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap character; and in amino acid sequences, U and * are acceptable letters (see below). Numerical digits are not allowed but are used in some databases to indicate the position in the sequence.
The nucleic acid codes supported are:
| Nucleic Acid Code | Meaning |
|---|---|
| A | Adenosine |
| C | Cytosine |
| G | Guanine |
| T | Thymidine |
| U | Uracil |
| R | G A (puRine) |
| Y | T C (pYrimidine) |
| K | G T (Ketone) |
| M | A C (aMino group) |
| S | G C (Strong interaction) |
| W | A T (Weak interaction) |
| B | G T C (not A) (B comes after A) |
| D | G A T (not C) (D comes after C) |
| H | A C T (not G) (H comes after G) |
| V | G C A (not T, not U) (V comes after U) |
| N | A G C T (aNy) |
| X | masked |
| - | gap of indeterminate length |
The amino acid codes supported are:
| Amino Acid Code | Meaning |
|---|---|
| A | Alanine |
| B | Aspartic acid or Asparagine |
| C | Cysteine |
| D | Aspartic acid |
| E | Glutamic acid |
| F | Phenylalanine |
| G | Glycine |
| H | Histidine |
| I | Isoleucine |
| K | Lysine |
| L | Leucine |
| M | Methionine |
| N | Asparagine |
| O | Pyrrolysine |
| P | Proline |
| Q | Glutamine |
| R | Arginine |
| S | Serine |
| T | Threonine |
| U | Selenocysteine |
| V | Valine |
| W | Tryptophan |
| Y | Tyrosine |
| Z | Glutamic acid or Glutamine |
| X | any |
| * | translation stop |
| - | gap of indeterminate length |
[edit] Sequence identifiers
The NCBI defined a standard for the unique identifier used for the sequence (SeqID) in the header line. The formatdb man page has this to say on the subject: "formatdb will automatically parse the SeqID and create indexes, but the database identifiers in the FASTA definition line must follow the conventions of the FASTA Defline Format."
However they do not give a definitive description of the FASTA defline format. An attempt to create such a format is given below.
GenBank gi|gi-number|gb|accession|locus EMBL Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
The vertical bars in the above list are not separators in the sense of the Backus-Naur form, but are part of the format.
[edit] File extension
There is no standard file extension for a text file containing FASTA formatted sequences. FASTA format files often have file extensions like .fa, .mpfa, .fna, .fsa, .fas or .fasta
[edit] HUPO-PSI Format
There are several pitfalls to the traditional FASTA format that this format is meant to solve:
- Definition lines vary widely for no good reason. This causes problems for end users who want to use these files with protein identification tools. The creators of these tools are faced with a significant challenge of either supporting all of these variations or enabling a user to cope with them.
- Same database processed in different search engines → different identifiers → difficult to map (P00761 vs. ALBU_HUMAN)
- Same protein in different databases can have very different identifiers (P00761 vs gi|3446572|sp|p00761 vs IPI:12345678)
- The information extracted from the FASTA formats is heterogeneous: parsability issues. Should come from the DB
- Description and availability of taxonomy (Latin names, common names, NCBI TaxID)
[edit] Header block
Includes information about the included database(s). All lines in the block start with the '#' character. One header term from the list below per line:
| 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= | Database 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. |
Example Header Block:
#\Dbcomponent=1 #\Name=UniProt_SwissProt #\PrimaryIdentifierType=sp_ac #\Version=52.3 #\ReleaseDate=20070425 #\NumberOfEntries=248942 #\Sequence_type=Protein_sequence #\Dbcomponent=2 #\Name=ENSEMBL #\PrimaryIdentifierType=sp_ac #\Version=12.45.3.2 #\ReleaseDate=20070425 #\NumberOfEntries=1234567 #\Sequence_type=Protein_sequence
[edit] Sequence header line
| 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) |
Example Protein Entry:
>sp_ac|P02769_WOSIG0 \ID=ALBU_BOVIN \DE="Serum albumin precursor (Allergen Bos d 6) (BSA)" \NCBITAXID=9913 \MODRES=(1|Acetyl) \VARIANT=(196|A|T) \LENGTH=589 RGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNELTEFAKTCV ADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPK LKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKG ACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLV TDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKECCDKPLLEKSHCIAEVEK DAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAKEYEA TLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKV PQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTK CCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKH KPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVVSTQTALA
[edit] See also
[edit] External links
- HUPO-PSI Standard FASTA Format describes another FASTA format as put forward by the Human Proteome Organisation's Proteomics Standards Initiative.
- Readseq sources for ReadSeq: converting sequence formats to FASTA
- Readseq online at IUBio
- Readseq online at BCM
- Sequence File-Format Converter Convert files to or from FASTA format
- GenBank to Fasta conventer - Poorly documented.
- UGENE DNA Export plugin A visual and easy to use environment to extract sequences from different file formats into FASTA files.
