ScanProsite
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ScanProsite tool
ScanProsite
This form requires to have JavaScript enabled to work correctly.
This form allows you to scan proteins for matches against the
PROSITE collection of motifs
as well as against your own patterns.
/cgi-bin/prosite/PSScan.cgi
Option 1 - Submit PROTEIN sequences to scan them against the PROSITE collection of motifs.
Submit protein sequences (up to 10) or a whole protein custom database (up to 16 MB in size) and scan it against the whole collection of PROSITE motifs. Doing so you have the possibility to exclude profiles from the scan and to run the scan at a high sensitivity.
/cgi-bin/prosite/PSScan.cgi
Option 2 - Submit MOTIFS to scan them against a PROTEIN sequence database.
Submit a PROSITE motif, a custom pattern or a combination of any of the latter and scan them against a protein database. The choice of protein database includes UniProtKB, PDB, a custom database or randomized database of the UniProtKB reviewed section. Doing so you can tune a number of parameters regarding the motif being scanned, such as the number of hits it must have in a sequence for a match to be reported or some criteria that the matched sequences must fulfill to be reported like for instance having a minimal size.
/cgi-bin/prosite/PSScan.cgi
Option 3 - Submit PROTEIN sequences and MOTIFS to scan them against each other.
Submit protein sequences (up to 10) or a whole protein custom database (up to 16 MB in size) and scan it against a motif or a combination of motifs of your choice. you. The motif or collection of motifs can be a PROSITE motif, a custom pattern or a combination of any of the latter. If you submit a PROSITE profile, you have the possibility for the scan to be performed at a high sensitivity.
STEP 1 - Submit PROTEIN sequences
[
help
]
Submit PROTEIN sequences (max. 10)
Examples
Submit a PROTEIN database (max. 16MB) for repeated scans (The data will be stored on our server for 1 month).
Supported input:
UniProtKB
accessions e.g.
P98073
or identifiers e.g.
ENTK_HUMAN
*
PDB
identifiers e.g.
4DGJ
Sequences in
FASTA format
*All UniProtKB/Swiss-Prot accessions/identifiers and all UniProtKB/TrEMBL accessions/identifiers of entries belonging to reference proteomes are accepted.
If you already have a code for your database, enter the code:
Otherwise,
upload your database as a FASTA file to obtain a code
STEP 2 - Select options
[
help
]
Exclude motifs with a high probability of occurrence
from the scan
Exclude profiles
from the scan
Run the scan at high sensitivity
(show weak matches for profiles)
STEP 1 - Enter a MOTIF or a combination of MOTIFS
Examples
[
help
]
PS00781
Supported input:
A PROSITE accession e.g.
PS50240
or identifier e.g.
TRYPSIN_DOM
Your own pattern e.g.
P-x(2)-G-E-S-G(2)-[AS]
A combination of PROSITE accessions/identifiers e.g.
PS50240 and PS50068
, e.g.
PS50240 and not ( PS00134 or PS00135 )
A combination of PROSITE accessions/identifiers and your own pattern e.g.
PS50240 and P-x(2)-G-E-S-G(2)-[AS]
» More
» Options
[
help
]
Mimimal number of hits per matched sequences
:
Profile option
Run the scan at a high sensitivity
(show weak matches for profiles)
Pattern options
Number of X characters in a scanned sequence that can be matched by a conserved position in a pattern:
Match mode
:
greedy, overlaps, no includes
greedy, overlaps, includes
greedy, no overlaps
not greedy, overlaps, no includes
not greedy, overlaps, includes
not greedy, no overlaps
STEP2 - Select a PROTEIN sequence database
[
help
]
UniProtKB
Swiss-Prot
Include isoforms
TrEMBL (sequences belonging to reference proteomes only)
PDB
Your protein database
If you already have a code for your database, enter the code:
Otherwise,
upload your database as a FASTA file to obtain a code
Randomized UniProtKB/Swiss-Prot
[
help
]
reversed
window20
Exclude fragments (concerns UniProtKB only)
» Filters
[
help
]
On length >= than:
On length <= than:
On taxonomy:
any taxonomical term e.g.
Homo sapiens
, e.g.
Fungi; Arthropoda
or corresponding
TaxID
e.g.
9606
, e.g.
4751; 6656
STEP 1 - Submit PROTEIN sequences
[
help
]
Submit PROTEIN sequences (max. 1'000)
Examples
Submit a PROTEIN database (max. 16MB) for repeated scans (The data will be stored on our server for 1 month).
Supported input:
UniProtKB
accessions e.g.
P98073
or identifiers e.g.
ENTK_HUMAN
*
PDB
identifiers e.g.
4DGJ
Sequences in
FASTA format
*All UniProtKB/Swiss-Prot accessions/identifiers and all UniProtKB/TrEMBL accessions/identifiers of entries belonging to reference proteomes are accepted.
If you already have a code for your database, enter the code:
Otherwise,
upload your database as a FASTA file to obtain a code
STEP 2 - Enter a MOTIF or a combination of MOTIFS
Examples
[
help
]
PS00781
Supported input:
A PROSITE accession e.g.
PS50240
or identifier e.g.
TRYPSIN_DOM
Your own pattern e.g.
P-x(2)-G-E-S-G(2)-[AS]
A combination of PROSITE accessions/identifiers e.g.
PS50240 and PS50068
, e.g.
PS50240 and not ( PS00134 or PS00135 )
A combination of PROSITE accessions/identifiers and your own pattern e.g.
PS50240 and P-x(2)-G-E-S-G(2)-[AS]
» More
» Options
[
help
]
Profile option
Run the scan at a high sensitivity
(show weak matches for profiles)
Pattern options
Number of X characters in a scanned sequence that can be matched by a conserved position in a pattern:
Match mode
:
greedy, overlaps, no includes
greedy, overlaps, includes
greedy, no overlaps
not greedy, overlaps, no includes
not greedy, overlaps, includes
not greedy, no overlaps
STEP 3 - Select output options and submit your job
Output format
:
Graphical view
Simple view
Text
FASTA
Table
Matchlist
Maximum number of displayed matches
:
1'000
10'000
100'000 (by email only)
If you select 100'000, results are returned by email and not all output formats are available.
Retrieve complete sequences
:
If you choose this option, not all output formats are available.
Receive your results by email
Email
:
Note that not all output formats are available for results returned by email.
Job title
:
If available, the job title will be included in the subject of the results email.
