IMGT Index

FASTA format

Definition and description

The FASTA format is a sequence format that begins with a single description line followed by lines of sequence data.
The FASTA format is used as query input for many bioinformatic tools such as BLAST, ClustalW, IMGT/V-QUEST etc.
The description line starts with a ">" symbol, followed by a sequence identifier (chosen by the user) without space. It is recommended that all lines of text be shorter than 80 characters in length. Blanks are ignored, dots (.), hyphens (-) or underscores (_) must be used to represent gaps. A FASTA file may contain many sequences in FASTA format, blank lines are not allowed in the middle of the FASTA input.

Examples of nucleotide sequences in FASTA format

in IMGT reference directory:
```
>M29672_IGHV1S1*01_Rajeri
	GCGGTCGTGCTGAATCAGAAACCGACC...GAGGCGGCAAAGTCTGGAGAGTCCCTCAAACTGACCTGTGTAACCAGCG
	GGTTCAGCCTCAGCAGCTCCAAC............GTGCATTGGGTGAAACAAGTCCCCGGGAAAGGGCTGGAGTGGGT
	GGCGATCATGTGGTATGATGATGACAAA.........GATTACGCGCCTGCCTTCAGC...GGCCGATTCACTGTTTCC
	AGG......GACAGCAGCAATGTCTATCTCCAAATGACCAACCTGAGTCTGGCCGACACGGCCACCTATTACTGTGCG
	
```
In this example, the description line comprises the IMGT/LIGM-DB sequence accession number (M29672), the allele name (TRDJ1*01), the abbreviation for the species (Rajeri) for Leucoraja erinacea (the abbreviation used by IMGT comprises the three first letters of the genus Latine name followed by the three first letters of the species Latin name).

in IMGT/LIGM-DB:

>M29672|REIGHA|R.erinacea Ig rearranged H-chain mRNA (V-D-J-C region).
	cccattcctggagtgtccaagtgtgtgtccgtgctcagagtgatgggggtcgctgtttat
	ctctgtctccttctgttctgtctgccaggcgttcgatccgcggtcgtgctgaatcagaaa
	ccgaccgaggcggcaaagtctggagagtccctcaaactgacctgtgtaaccagcgggttc
	agcctcagcagctccaacgtgcattgggtgaaacaagtccccgggaaagggctggagtgg
	gtggcgatcatgtggtatgatgatgacaaagattacgcgcctgccttcagcggccgattc
	actgtttccagggacagcagcaatgtctatctccaaatgaccaacctgagtctggccgac
	acggccacctattactgtgcggcagccatggggggctctatatactggcttgagtactgg
	ggtgcaggaacctcgctgacagtgacttcagaggatgtggttttgccttcagtccacatc
	acctcttcctgcaacacggaatctggccaagagatcagcatcctctgtctggtcaaggac
	tacctgcctgaggtcatcagtcagacatggtccaccagcagtggggtcatcaacaatgga
	ataacaaagtacccaccagtgttgggacaaaacaagaagtacacaatgagcagcttgctg
	cgagtctctgtagcagattggaacaggaaaacctactactgcaaggcagggtacaagccg
	gacaacatggtgaaaacggagatccagaagcctcaagccccacagctcatcccccttgtt
	ccatctccggagactctccacaatcaaacaactgctgtcctgggctgcatgatatctgga
	ttctctcctgacaatattaaagtttcctggaaaaaagctggacttaatcaagcgggcgtc
	gttctcccatccactccgagaactaacggtggatttgaaacagttgcttacctgccgttg
	aatgtggaggaatggaccaacaaacaggaatatacttgtgaagtgacccacgcaccttcc
	ggcttcagcgacaagatcaacatgagatatcaagagggtggaaaatgtcccggctgttcg
	aagtgtctgccgaagttcatctaccagagtaatctcaatgtgtcgttctcagatggttct
	acccagcagtatcattgttgggcaggaaagtgtgaaataaagtaattggctgc

In this example, the description line comprises the IMGT/LIGM-DB sequence accession number (M29672), the mnemonic (REIGHA), the definition (extracted from EMBL).

in IMGT/GENE-DB:

>AE000658|TRAV4*01|Homo sapiens|F|V-REGION
	cttgctaagaccacccag...cccatctccatggactcatatgaaggacaagaagtgaac
	ataacctgtagccacaacaacattgctacaaatgattat...............atcacg
	tggtaccaacagtttcccagccaaggaccacgatttattattcaaggatacaagaca...
	...............aaagttacaaacgaa.....................gtggcctcc
	ctgtttatccctgccgacagaaagtccagcactctgagcctgccccgggtttccctgagc
	gacactgctgtgtactactgcctcgtgggtgaca

In this example, the description line comprises the IMGT/LIGM-DB sequence accession number (AE000658), the allele name (TRAV4*01), the species (Homo sapiens), the functionality of the allele (F for Functional), the label of the coding region (V-REGION). The word "partial" is then added when the coding region is partial in 5' or 3'.