The ScanProsite tool allows to scan protein sequence(s) against the PROSITE database. The user can provide either an UniProt Knowledgebase or Protein Data Bank (PDB) sequence identifier(s) (AC(s) or/and ID(s)) or a sequence(s) in fasta or UniProtKB format. By default the motifs to search for the occurrence are PROSITE patterns and profiles. PROSITE profiles may optionally be excluded.

The ScanProsite tool also allows to search for hits by specific motif(s) in protein sequence database(s). The motif(s) to search for hits may either be PROSITE pattern(s) and/or profile(s), or provided by the user (Note that the program PRATT allows to generate your own patterns). By default, the protein sequence database to be scanned is UniProtKB/Swiss-Prot, including splice variants. Others protein sequence databases may also be scanned, such as UniProtKB/TrEMBL and/or PDB. Furthermore, you can adjust your search limits by specifying filter(s) and pattern option(s).

Finally, the ScanProsite tool allows to scan protein sequence(s) for the occurrence of motif(s).

ScanProsite may be used alternatively into two modes a quick scan mode and an advanced scan mode.
(For programmatic access, see ScanProsite REST web service )

You may enter one or more sequences [1 by line and maximum 8 sequences] to scan against PROSITE patterns and profiles.

If you want to scan your sequence against all PROSITE motifs:

Paste your sequence in the text box . The sequence must be either raw (only amino acids, 1 letter code, no numbers), in fasta format (e.g. for: P01621), or in UniProtKB format (e.g. for: P01621). Click on 'Scan'.

If you want to scan a UniProtKB (Swiss-Prot or TrEMBL)/PDB sequence against all PROSITE motifs :

Paste your sequence identifier, either: AC (e.g. P01621) or ID (e.g. KV3C_HUMAN) in the text box. Click on 'Scan'.
In both cases the sequence(s) will be scanned against all PROSITE motifs. If you want to scan a sequence against all PROSITE motifs except the ones with a high probability of occurence, please select the suitable check box under the scan button. Hits from PROSITE profiles with a score greater than the profile defined cutoff score will be shown. Results will be diplayed in HTML 'graphical rich view' mode.

If you want to scan your sequence against all PROSITE motifs :

Paste your sequence in the text box of the section 'Sequence(s) to be scanned'. The sequence must be either raw (only amino acids, 1 letter code, no numbers), in fasta format, or in UniProtKB format.
Now click on 'START THE SCAN'. Your sequence will be scanned against all PROSITE motifs except the ones with a high probability of occurence. By default, hits from PROSITE profiles with a score greater than the profile defined cutoff score will be shown, and results will be diplayed in HTML 'graphical rich view' mode. But you can alter these parameters.

If you want to scan a UniProtKB (Swiss-Prot or TrEMBL)/PDB sequence against all PROSITE motifs :

Enter the sequence identifier, either: AC (e.g. P05130) or ID (e.g. ENTK_HUMAN), or paste the sequence in the text box of the section 'Sequence(s) to be scanned'.
Click on 'START THE SCAN' button...

If you want to scan the UniProt Knowledgebase with a particular PROSITE motif :

Enter the PROSITE motif identifier, either: AC (e.g. PS50240) or ID (e.g.TRYPSIN_DOM).
Click on 'START THE SCAN' button...

If you want to scan the UniProt Knowledgebase with a particular pattern :

Type your pattern in the text box of the section 'Motifs(s) to scan for'. You should use the PROSITE pattern syntax and type your pattern on one line (don't type 'enter'/'return' inside the pattern).
Click on 'START THE SCAN' button...

Scan with multiple sequences or motifs

Multiple sequences :

You can scan multiple sequences at the same time (maximum 8 sequences if the scan is against all PROSITE motifs, 16 if the scan is against more than 1 motifs, 1000 if against a single motif). Put each UniProtKB (Swiss-Prot or TrEMBL) and/or PDB sequence identifier on a new line. If you want to scan several of your own sequences, you must enter them in fasta or UniProtKB format.

Multiple motifs :

You can scan against multiple motifs at the same time (maximum 8 motifs if the scan is against (a) protein database(s), or 16 if the scan is against (a) particular protein(s)). Put each PROSITE motif identifier or pattern on a new line. Hits from any of those motifs will be shown (logical OR).

Pattern syntax

1. The standard IUPAC one-letter codes for the amino acids are used in PROSITE.
2. The symbol `x' is used for a position where any amino acid is accepted.
3. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square brackets `[ ]'. For example: [ALT] stands for Ala or Leu or Thr.
4. Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met.
5. Each element in a pattern is separated from its neighbor by a `-'.
6. Repetition of an element of the pattern can be indicated by following that element with a numerical value or, if it is a gap ('x'), by a numerical range between parentheses.
   

   Examples:

   x(3) corresponds to x-x-x

   x(2,4) corresponds to x-x or x-x-x or x-x-x-x

   A(3) corresponds to A-A-A

   Note: You can only use a range with 'x', i.e. A(2,4) is not a valid pattern element.

7. When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol. In some rare cases (e.g. PS00267 or PS00539), '>' can also occur inside square brackets for the C-terminal element. 'F-[GSTV]-P-R-L-[G>]' means that either 'F-[GSTV]-P-R-L-G' or 'F-[GSTV]-P-R-L>' are considered.

Database randomization

Note: can only be used in scans against patterns (no profile allowed).

It is often useful to be able to search a pattern against a random database in order to evaluate its specificity. It is desirable that the database be not completely random, but comparable to the databases which are to be scanned in terms of amino acid frequency and local compositional bias. ScanProsite can randomize the scanned databases on the fly, using one of two methods:

• reverse sequences - randomize by taking the reverse sequence of each individual entry
• shuffle - randomize by local shuffling of the residues in windows of 20 residues

The reverse sequences method is generally recommendable, but it is not adapted for patterns which are strongly enriched in one amino acid (e.g. C-C-C-[LIV]) or which are palindromic (e.g. M-L-L-M). Sample randomized databases and the scripts used to generate them are available at ftp://ftp.isrec.isb-sib.ch/pub/databases/shuffled/.

Pattern matching mode

Three parameters allow to finely tune the behaviour of the pattern-matching engine. These are :

greed :

extend at most variable-length pattern elements

overlap :

allow partially overlapping matches

include :

allow matches included within one another (implies overlap)

The default behavior is greedy, allows overlaps but not included matches. This means that two overlapping matches are rejected if one is entirely contained within the other.

For example, consider the sequence ``ABACADAEAFA'' and the simple pattern ``A-x(1,3)-A''. The six possible combinations of the switches produce the following results:

• greed=1, overlap=1, include=0 (default) : 4 matches

    ABACADAEAFA
    ooooo......
    ..ooooo....
    ....ooooo..
    ......ooooo

• greed=1, overlap=1, include=1 : 5 matches

    ABACADAEAFA
    ooooo......
    ..ooooo....
    ....ooooo..
    ......ooooo
    ........ooo

• greed=1, overlap=0 : 2 matches

    ABACADAEAFA
    ooooo......
    ......ooooo

• greed=0, overlap=1, include=0 or 1 : 5 matches

    ABACADAEAFA
    ooo........
    ..ooo......
    ....ooo....
    ......ooo..
    ........ooo

• greed=0, overlap=0 : 3 matches

    ABACADAEAFA
    ooo........
    ....ooo....
    ........ooo

Filters

You can adjust the ScanProsite parameters by specifying filters on taxonomic lineage (OC) or species (OS). The taxonomy database used in PROSITE is NEWT. In case you want to define a filter including different taxa/species, separate them with a semicolon (e.g. Eukaryota;Escherichia coli;). Filters can not be specifyed for PDB sequences.

Exclude motifs with a high probability of occurrence :

Does not scan against motifs with a high probability of occurrence.