Protein Sequence Format

1. FASTA sequence:

   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 sequencein FASTA format is:

       >gi|129295|sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED)
       QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE
       KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS
       VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP
       FLFLIKHNPTNTIVYFGRYWSP
       

2. Bare Sequence:

   This may be just lines of sequence data, without the FASTA definition line, e.g.:

   QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE
   KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS
   VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP
   FLFLIKHNPTNTIVYFGRYWSP 
   
   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