Rules for pattern syntax for PHI-BLAST.

The syntax for patterns in PHI-BLAST follows the conventions of PROSITE. When using the stand-alone program, it is permissible to have multiple patterns in a file separated by a blank line between patterns. When using the Web-page only one pattern is allowed per query.

Valid protein characters for PHI-BLAST patterns: 

    ABCDEFGHIKLMNPQRSTVWXYZU
Valid DNA characters for PHI-BLAST patterns: 
    ACGT
Other useful delimiters: 
    [ ]    means any one of the characters enclosed in the brackets
        e.g., [LFYT] means one occurrence of L or F or Y or T
    -      means nothing (this is a spacer character used by PROSITE)
    x with nothing following means any residue
    x(5)  means 5 positions in which any residue is allowed (and similarly for any other
          single number in parentheses after x)
    x(2,4) means 2 to 4 positions where any residue is allowed,
           and similarly for any other two numbers separated by a comma;
           the first number should be < the second number.           
    >      can occur only at the end of a pattern and means nothing
           it may occur before a period
           (another spacer used by PROSITE)

    .      may be used at the end of the pattern and means nothing
When using the stand-alone program, the pattern should be in a file, with the first line starting: 
 ID
followed by 2 spaces and a text string givign the pattern a name.

There should also be a line starting 

 PA
followed by 2 spaces followed by the pattern description.

All other PROSITE codes in the first two columns are allowed, but only the HI code, described below is relevant to PHI-BLAST.

Here is an example from PROSITE. 

ID   CNMP_BINDING_2; PATTERN.
AC   PS00889;
DT   OCT-1993 (CREATED); OCT-1993 (DATA UPDATE); NOV-1995 (INFO UPDATE).
DE   Cyclic nucleotide-binding domain signature 2.
PA   [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].
NR   /RELEASE=32,49340;
NR   /TOTAL=57(36); /POSITIVE=57(36); /UNKNOWN=0(0); /FALSE_POS=0(0);
NR   /FALSE_NEG=1; /PARTIAL=1;
CC   /TAXO-RANGE=??EP?; /MAX-REPEAT=2;
The line starting 
    ID
gives the pattern a name. The lines starting 
     AC, DT, DE, NR, NR, CC
are relevant to PROSITE users, but irrelevant to PHI-BLAST. These lines are tolerated, but ignored by PHI-BLAST.

The line starting 

     PA
describes the pattern as:
      one of LIVMF
followed by
      G
followed by
      E
followed by 
      any single character
followed by
      one of GAS
followed by
      one of LIVM
followed by 
      any 5 to 11 characters
followed by
      R
followed by
      one of STAQ
followed by
      A
followed by
      any single character
followed by
      one of LIVMA
followed by
      any single character
followed by 
      one of STACV
In this case the pattern ends with a period. It can end with nothing after the last specifying symbol or any number of > signs or periods or combination thereof.

Here is another example, illustrating the use of an HI line. 

ID    ER_TARGET; PATTERN.
PA  [KRHQSA]-[DENQ]-E-L>.
HI (19 22)
HI (201 204)
In this example, the HI lines specify that the pattern occurs twice, once from positions 19 through 22 in the sequence and once from positions 201 through 204 in the sequence. These specifications are relevant when stand-alone PHI-BLAST is used with the "seedp" option, in which the interesting occurrences of the pattern in the sequence are specified. In this case the HI lines specify which occurrence(s) of the pattern should be used to find good alignments.

In general, the seedp option is more useful than the standard patternp option ONLY when the pattern occurs K > 1 times in the sequence AND the user is interested in matching to J < K of those occurrences. Then using the HI lines enables the user to specify which occurrences are of interest.