to predict protein function , assign family identity or detect remote homologues , searches against signature databases , also known as secondary databases ( 1 ) , are essential .
scanprosite provides a web interface to identify protein matches against signatures from the prosite database ( 2 ) .
the prosite database consists of a large collection of biologically meaningful signatures that are described as patterns ( regular expressions ) , used for short motif detection , or generalized profiles ( weight matrices ) for sensitive detection of larger domains .
all signatures are built from manually derived alignments and are provided with extensive manually curated documentation ( taxonomic occurrence , function , etc . ) .
prosite signatures form a high quality collection and are closely tied to the uniprotkb / swiss - prot ( 3,4 ) annotation process . in addition , each prosite profile is associated with a manually curated annotation template called prorule ( 5 ) .
these rules are used internally , by the swiss - prot group , to automate prosite domain annotation of uniprotkb / swiss - prot entries .
a number of prorules define biologically meaningful information about specific residues within their associated domain .
this positional information ( derived from the mapping of significant residues to the profile ) is provided in the form of contextual feature annotation blocks : certain conditions  a specific sequence , the presence of other features  must be fulfilled for the annotation block to be applied , hence for the feature to be predicted .
consequently , those prorules add pattern - like discriminativity with motif - specific information to their associated profile , allowing the detection of intra - domain features , such as active sites , binding sites or disulfide bridges .
combining the sensitivity of profiles with the specificity of motif detection enhances the accuracy of signature based functional predictions .
the scanprosite rich result viewer detects those intra - domain features by evaluating  on the fly  associated prorules on matched profiles and integrates them with the match results .
the interproscan tool ( ) can scan sequences against prosite signatures (  profilescan application ) , but does not provide intra - domain feature detection ,  rich graphical output and extensive scanning options including scans against custom user patterns .
scanprosite was implemented in perl , and is served through an apache web server running on a unix operating system .
care was taken to ensure that all generated pages are fully standards - compliant ( valid html 4.01 transitional ) .
the pre - computed match database and the prorule database are stored in a postgresql database .
program output can either be displayed in the web browser ( interactive mode ) , or sent by email ( batch mode ) .
the rich view output mode uses standard dhtml ( html , css , javascript ) , and no additional plugins are required .
the job submission starting page is located at   on the expasy web server ( 7 ) . here
the user has to enter sequence and/or signature data , choose the output format , and specify various scan behavior options before launching the analysis job .
user sequences and/or uniprotkb sequences / databases can be scanned against user patterns and/or prosite signatures / database .
multiple sequences and/or signatures can be submitted at once ( maximum : 8 for scans against databases , otherwise 16 ) . in this case
, any specified signature will be searched against any specified sequence ( logical or ) . for scans against protein databases
, the search space can be reduced to specific taxa , and/or to entries containing a specific term in their description ( uniprotkb de line ) .
protein databases can be randomized ( reversed or shuffled ) to evaluate user pattern significance ( 8) .
pattern matching mode can be altered ( see aforementioned online documentation page under  pattern matching mode ) .
users can choose to retrieve full sequences ( in fasta format ) of matched proteins together with signature match results .
unspecific signatures with a high probability of occurrence ( see prosite user manual at ) can be excluded ( this option is activated by default ) .
users can also choose to include low level profile matches ( with score smaller than the high confidence - level 0 - cut - off ) in the output ( this option is not activated by default ) . to save bandwidth and computing power
, there is a limit on the number of distinct matching sequences and total matches that can be displayed .
users can select the maximum of matching sequences ( by default , not more than 5000 matches in 1000 sequences will be displayed ) .
a maximum of 10 000 or 100 000 sequences ( 50 000 or 500 000 signature matches ) can only be requested in the non - interactive 
instructions for simple programmatic access ( text / plain output ) are available on demand ( email : prosite@expasy.org ) .
once the job has been submitted , the data are posted to an application that will make use of pre - computed matches whenever possible .
results are retrieved from an internal relational database that stores matches of all prosite signatures ( except the  unspecific signatures with a high probability of occurrence ) against the uniprot knowledgebase , including additional splice variants , and pdb ( 9 ) . for analyses where no pre - computed results are available ( e.g. on user sequences , user patterns or 
unspecific signatures ) a real - time sequence analysis is performed using the ps_scan program ( 10 ) .
users requiring high - throughput sequence analysis or who wish to use custom databases can download ps_scan stand - alone tool at .
available results are pooled and saved ( for 12 h ) on the server , for later use by the rich viewer .
the detection of intra - domain features is performed on the fly by the rich viewer over the matching domains ( and is therefore only available in the rich view output mode , see below ) .
profile match regions are evaluated for fulfillment of feature detection conditions specified in the associated prorules .
the features themselves are represented in the prorule as uniprotkb / swiss - prot annotation blocks that are applied when detection conditions are fulfilled .
the feature annotation blocks and their detection conditions are retrieved from an internal database storing a relational representation of the prorules .
detection conditions can be : specific amino acids inside the domain ( regular expressions that can be grouped by logical operators ) , groups of conditions in which all conditions must be fulfilled ( e.g. catalytic triad of trypsin protease ) . to date , intra - domain feature detection is performed for 136 of the 595 prosite profiles ( prosite release 19.20 , of 07-feb-2006 ) . predicted features include ( table 1 ) : binding sites for chemical groups ( such as heme , atp ) , glycosylation site , disulfide bridges , dna binding sites , metal ion binding sites , post - translational modification sites ( such as phosphotyrosine , phosphoserine ) etc .
the system can be easily extended to use other uniprotkb / swiss - prot feature types . in interactive mode ,
once the analysis is completed , the results will be directly displayed in the selected output view mode inside user 's web browser . in batch mode
, results in simple text format are emailed to the user - specified email address , together with a link to visualize the results , stored on the server , through the rich viewer .
in rich view and simple html view modes , matching uniprot knowledgebase protein entries are shown with a link to their expasy niceprot view , their description and organism . moreover , for entries that have associated pdb structures , there are links to interactive 3d views highlighting the match region over the 3d structure .
the rich view can be accessed , as a link , from any other views .
the rich view output mode provides an interactive match viewer and intra - domain feature predictor / viewer in both text and graphical forms .
the graphical view is a symbolic representation of matches , inspired by smart ( 11 ) and predicted features in a high quality image ( portable network graphics format ) that can be used in presentations or papers ( figure 1 ) .
the view is generated by a specific web tool that uses saved results allowing delayed results examination for up to 12 h after the initial scan ( useful in batch mode ) .
in addition to the match results , intra - domain feature evaluations ( if any ) are detailed .
for each evaluated feature , its uniprotkb / swiss - prot feature key , boundaries , description , the detection conditions and the condition group ( if any ) , are displayed .
features with fulfilled conditions are shown under  predicted features and integrated into the graphical representation . features with unfulfilled conditions are shown under 
absent feature. the rich view also provides interactive match and feature highlighting , on results of a single sequence scan , with most web browsers e.g. mozilla , firefox , netscape , opera , provided javascript is enabled ( with internet explorer this javascript functionality is too slow and was disabled ) . moving the cursor over a feature information line will highlight its position ( green for predicted features , gray for absent features ) in both the match sequence and the protein sequence . moving
the cursor over a match in the graphical view or the text view will highlight in yellow its position in the protein sequence .
the job submission starting page is located at   on the expasy web server ( 7 ) . here
the user has to enter sequence and/or signature data , choose the output format , and specify various scan behavior options before launching the analysis job .
user sequences and/or uniprotkb sequences / databases can be scanned against user patterns and/or prosite signatures / database .
multiple sequences and/or signatures can be submitted at once ( maximum : 8 for scans against databases , otherwise 16 ) . in this case
, any specified signature will be searched against any specified sequence ( logical or ) . for scans against protein databases ,
the search space can be reduced to specific taxa , and/or to entries containing a specific term in their description ( uniprotkb de line ) .
protein databases can be randomized ( reversed or shuffled ) to evaluate user pattern significance ( 8) .
pattern matching mode can be altered ( see aforementioned online documentation page under  pattern matching mode ) .
users can choose to retrieve full sequences ( in fasta format ) of matched proteins together with signature match results .
unspecific signatures with a high probability of occurrence ( see prosite user manual at ) can be excluded ( this option is activated by default ) .
users can also choose to include low level profile matches ( with score smaller than the high confidence - level 0 - cut - off ) in the output ( this option is not activated by default ) . to save bandwidth and computing power
, there is a limit on the number of distinct matching sequences and total matches that can be displayed .
users can select the maximum of matching sequences ( by default , not more than 5000 matches in 1000 sequences will be displayed ) .
a maximum of 10 000 or 100 000 sequences ( 50 000 or 500 000 signature matches ) can only be requested in the non - interactive 
instructions for simple programmatic access ( text / plain output ) are available on demand ( email : prosite@expasy.org ) .
once the job has been submitted , the data are posted to an application that will make use of pre - computed matches whenever possible .
results are retrieved from an internal relational database that stores matches of all prosite signatures ( except the  unspecific signatures with a high probability of occurrence ) against the uniprot knowledgebase , including additional splice variants , and pdb ( 9 ) . for analyses where no pre - computed results are available ( e.g. on user sequences , user patterns or 
unspecific signatures ) a real - time sequence analysis is performed using the ps_scan program ( 10 ) .
users requiring high - throughput sequence analysis or who wish to use custom databases can download ps_scan stand - alone tool at .
available results are pooled and saved ( for 12 h ) on the server , for later use by the rich viewer .
the detection of intra - domain features is performed on the fly by the rich viewer over the matching domains ( and is therefore only available in the rich view output mode , see below ) .
profile match regions are evaluated for fulfillment of feature detection conditions specified in the associated prorules .
the features themselves are represented in the prorule as uniprotkb / swiss - prot annotation blocks that are applied when detection conditions are fulfilled .
the feature annotation blocks and their detection conditions are retrieved from an internal database storing a relational representation of the prorules .
detection conditions can be : specific amino acids inside the domain ( regular expressions that can be grouped by logical operators ) , groups of conditions in which all conditions must be fulfilled ( e.g. catalytic triad of trypsin protease ) . to date , intra - domain feature detection is performed for 136 of the 595 prosite profiles ( prosite release 19.20 , of 07-feb-2006 ) . predicted
features include ( table 1 ) : binding sites for chemical groups ( such as heme , atp ) , glycosylation site , disulfide bridges , dna binding sites , metal ion binding sites , post - translational modification sites ( such as phosphotyrosine , phosphoserine ) etc .
the system can be easily extended to use other uniprotkb / swiss - prot feature types .
in interactive mode , once the analysis is completed , the results will be directly displayed in the selected output view mode inside user 's web browser . in batch mode ,
results in simple text format are emailed to the user - specified email address , together with a link to visualize the results , stored on the server , through the rich viewer . in rich view and simple html view modes , matching uniprot knowledgebase protein entries are shown with a link to their expasy niceprot view , their description and organism .
moreover , for entries that have associated pdb structures , there are links to interactive 3d views highlighting the match region over the 3d structure .
the rich view can be accessed , as a link , from any other views .
the rich view output mode provides an interactive match viewer and intra - domain feature predictor / viewer in both text and graphical forms .
the graphical view is a symbolic representation of matches , inspired by smart ( 11 ) and predicted features in a high quality image ( portable network graphics format ) that can be used in presentations or papers ( figure 1 ) .
the view is generated by a specific web tool that uses saved results allowing delayed results examination for up to 12 h after the initial scan ( useful in batch mode ) .
in addition to the match results , intra - domain feature evaluations ( if any ) are detailed .
for each evaluated feature , its uniprotkb / swiss - prot feature key , boundaries , description , the detection conditions and the condition group ( if any ) , are displayed .
features with fulfilled conditions are shown under  predicted features and integrated into the graphical representation .
absent feature. the rich view also provides interactive match and feature highlighting , on results of a single sequence scan , with most web browsers e.g. mozilla , firefox , netscape , opera , provided javascript is enabled ( with internet explorer this javascript functionality is too slow and was disabled ) . moving the cursor over a feature information line will highlight its position ( green for predicted features , gray for absent features ) in both the match sequence and the protein sequence . moving the cursor over a match in the graphical view or
we have described the current state of the scanprosite tool . the new implementation  online since summer 2004brings the use of pre - computed matches whenever possible , the detection of intra - domain biological features , a new graphical result representation and an interactive result viewer .
prosite , through scanprosite , provides broad intra - domain feature prediction via a flexible context - dependent annotation transfer system . associating domain detection with an automated annotation system
uniprotkb / swiss - prot features that can be predicted through scanprosite ( prosite release 19.20 , of 07-feb-2006 ) see uniprotkb / swiss - prot user manual at .
 scanprositeis a new and improved version of the web - based tool for detecting prosite signature matches in protein sequences . for a number of prosite profiles 
 , the tool now makes use of prorules  context - dependent annotation templates  to detect functional and structural intra - domain residues . 
 the detection of those features enhances the power of function prediction based on profiles . 
 both user - defined sequences and sequences from the uniprot knowledgebase can be matched against custom patterns , or against prosite signatures . to improve response times , 
 matches of sequences from uniprotkb against prosite signatures are now retrieved from a pre - computed match database . 
 several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results . 
INTRODUCTION
DESIGN AND IMPLEMENTATION
Input form
Sequence analysis
ScanProsite output
CONCLUSIONS
Figures and Tables