The BLAST 'Search' box accepts a number of different types of input and automatically determines the format. To allow this feature there are certain conventions required with regard to the input of identifiers (e.g., accessions or gi's). These are described in 3.) below. Accepted input types are:

1.) FASTA:

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

Blank lines are not allowed in the middle of FASTA input.

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

2.) Bare Sequence.

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

QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP FLFLIKHNPTNTIVYFGRYWSP

It can also be sequence interspersed with numbers and/or spaces, such as the sequence portion of a GenBank/GenPept flatfile report:

  1 qikdllvsss tdldttlvlv naiyfkgmwk tafnaedtre mpfhvtkqes kpvqmmcmnn
 61 sfnvatlpae kmkilelpfa sgdlsmlvll pdevsdleri ektinfeklt ewtnpntmek
121 rrvkvylpqm kieekynlts vlmalgmtdl fipsanltgi ssaeslkisq avhgafmels
181 edgiemagst gviedikhsp eseqfradhp flflikhnpt ntivyfgryw sp

Blank lines are not allowed in the middle of bare sequence input.

3.) Identifiers.

Normally these are simply accession, accession.version or gi's (e.g., p01013, AAA68881.1, 129295), but a bar-separated NCBI sequence identifier (e.g., gi|129295) will also be accepted. These NCBI sequence identifiers have a very specific syntax described in Appendix B of ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.txt The identifier may consist of only one token (i.e., word). Spaces between letters in the input will cause it to be treated as bare sequence (spaces before or after the identifier are allowed). Examples of illegal input are:

ACCESSION P01013 AAA68881. 1 gi| 129295

For the first example "ACCESSION" must be removed, in the second example there is a space before the version number of the accession, in the third example there is a space after the bar ("|").

For MegaBlast, where more than one query may be specified, each identifier should be on a separate line.

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Revised January 21, 2000