FASTA ID Specification

The V and J segment reference sequences must be provided in FASTA format. The FASTA sequence IDs must contain the following information, separated by | characters:

The gene, i.e. TRB, IGH, etc
The segment type, either V or J
The segment ID
The allele ID
The position of the first base of the Cys (or Phe) triplet (counting from 0)

Both the V and J segments have to be provided in the same file. Such a file might look like this:

...
>TRB|V|9|02|270
gattctggagtcacacaaaccccaaagcacctgatcacagcaactggacagcgagtgacg
ctgagatgctcccctaggtctggagacctctctgtgtactggtaccaacagagcctggac
cagggcctccagttcctcattcactattataatggagaagagagagcaaaaggaaacatt
cttgaacgattctccgcacaacagttccctgacttgcactctgaactaaacctgagctct
ctggagctgggggactcagctttgtatttctgtgccagcagcgtag
>TRB|V|9|03|270
gattctggagtcacacaaaccccaaagcacctgatcacagcaactggacagcgagtgacg
ctgagatgctcccctaggtctggagacctctctgtgtactggtaccaacagagcctggac
cagggcctccagttcctcattcaatattataatggagaagagagagcaaaaggaaacatt
cttgaacgattctccgcacaacagttccctgacttgcactctgaactaaacctgagctct
ctggagctgggggactcagctttgtatttctgtgccagcagc
>TRB|J|1-1|01|17
tgaacactgaagctttctttggacaaggcaccagactcacagttgtag
>TRB|J|1-2|01|17
ctaactatggctacaccttcggttcggggaccaggttaaccgttgtag
...