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4-5] FASTA format description
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. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA format is:
>gi|532319|pir|TVFV2E|TVFV2E envelope protein ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL LAAVEAQQQMLKLTIWGVK
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 of indeterminate length; and in amino acid sequences, U and * are acceptable letters (see below). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown nucleic acid residue or X for unknown amino acid residue).
The nucleic acid codes supported are:
A --> adenosine           M --> A C (amino)         C --> cytidine            S --> G C (strong)        G --> guanine            W --> A T (weak)         T --> thymidine           B --> G T C         U --> uridine             D --> G A T         R --> G A (purine)        H --> A C T         Y --> T C (pyrimidine)    V --> G C A         K --> G T (keto)          N --> A G C T (any)      -  gap of indeterminate length
For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:
A  alanine                         P  proline     B  aspartate or asparagine         Q  glutamine     C  cystine                         R  arginine     D  aspartate                       S  serine     E  glutamate                       T  threonine     F  phenylalanine                   U  selenocysteine     G  glycine                        V  valine     H  histidine                       W  tryptophan     I  isoleucine                      Y  tyrosine     K  lysine                          Z  glutamate or glutamine     L  leucine                        X  any     M  methionine                      *  translation stop     N  asparagine                      -  gap of indeterminate length
Article last modified on 2014-04-08 11:00:54 by lyang; viewed 1921 times; Category: User Documentation; Topic: Tools & Downloa

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