Introduction
Pratt - Pattern Matching. An important problem in sequence analysis is to find patterns matching sets or subsets of sequences. This tool allows the user to search for patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.
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How to Access Pratt
Pratt can be accessed via
Web Form
Web interface for Pratt is available at : https://www.ebi.ac.uk/Tools/pfa/pratt/
How to use this tool
Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.
Each tool has at least 2 steps, but most of them have more:
- The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
- In the following steps, the user has the possibility to change the default tool parameters
- And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server
Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.
Step 1 - Input Sequences
Input Sequence
The input set of up to 100 sequences can be entered directly into this form. The sequences can be in FASTA or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. (See example input formats). Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.
Sequence File Upload
A file containing up to 100 valid sequences in FASTA or UniProtKB/Swiss-Prot format can be used as input. (See example input formats). Word processor files may yield unpredictable results as hidden/control characters may be present. It is best to save files with the Unix format option to avoid hidden Windows characters.
Step 2 - Set alignment options
minPerc
Set the minimum percentage of the input sequences that should match a pattern (C%). If you set this to, say 80, Pratt will only report patterns matching at least 80 % of the sequences input.
Default value is: 100
Pattern Position
Pattern position in sequence (PP parameter)
| Pattern Position | Abbreviation |
|---|---|
| off | off |
| complete | complete |
| start | start |
Default value is: off
Max Pattern Length
Maximum pattern length (PL parameter) allows you to set the maximum length of a pattern. The length of the pattern C-x(2,4)-[DE] is 1+4+1=6. The memory requirement of Pratt depends on L; a higher L value gives higher memory requirement.
Default value is: 50
Max Num Pattern Symbols
Maximum number of pattern symbols (PN parameter). Using this you can set the maximum number of symbols in a pattern. The pattern C-x(2,4)-[DE] has 2 symbols (C and [DE]). When PN is increased, Pratt will require more memory.
Default value is: 50
Max Num Wildcard
Maximum length of a widecard (x). Using this option you can set the maximum length of a wildcard (PX parameter). Increasing this will increase the time used by Pratt, and also slightly the memory required.
Default value is: 5
Max Num Flex Spaces
Maximum length of flexible spaces. Using this option you can set the maximum number of flexible wildcards (matching a variable number of arbitrary sequence symbols) (FN parameter). Increasing this will increase the time used by Pratt.
Default value is: 2
Max Flexibility
Maximum flexibility. You can set the maximum flexibility of a flexible wildcard (matching a variable number of arbitrary sequence symbols) (FL parameter). For instance x(2,4) and x(10,12) has flexibility 2, and x(10) has flexibility 0. Increasing this will increase the time used by Pratt.
Default value is: 2
Max Flex Product
Maximum flex. product. Using this option you can set an upper limit on the product of a flexibilities for a pattern (FP parameter). This is related to the memory requirements of the search, and increasing the limit, increases the memory usage.
Default value is: 10
Pattern Symbol File
Pattern Symbol File (BI parameter)
Default value is: Off [false]
Num Pattern Symbols
Number of pattern symbols used in the initial search (BN parameter).
Default value is: 20
Pattern Restriction File
Pattern restriction file. The restriction file limits the sequence range via the start/end parameter and is in the format ">Sequence (start, end)". If parameter PP is off, the restiction file will be ignored.
Pattern Scoring
Pattern scoring (S parameter)
| Pattern Scoring | Abbreviation |
|---|---|
| info | info |
| mdl | mdl |
Default value is: info
Pattern Graph
Pattern Graph (G parameter) allows the use of an alignment or a query sequence to restrict the pattern search.
| Pattern Graph | Abbreviation |
|---|---|
| seq | seq |
Default value is: seq
Search Greediness
Using the greediness parameter (E) you can adjust the greediness of the search. Setting E to 0 (zero), the search will be exhaustive. Increasing E increases the greediness, and decreases the time used in the search.
Default value is: 3
Pattern Refinement
Pattern Refinement (R parameter). When the R option is switched on, patterns found during the initial pattern search are input to a refinement algorithm where more ambiguous pattern symbols can be added.
Default value is: Off [false]
Gen Ambig Symbols
Generalise ambiguous symbols (RG parameter). If the RG option is switched on, then ambiguous symbols listed in the symbols file are used. If RG is off, only the letters needed to match the input sequences are included in the ambiguous pattern positions.
Default value is: Off [false]
Pattern Format
PROSITE Pattern Format (OP parameter). When switched on, patterns will be output in PROSITE style (for instance C-x(2,4)-[DE]). When switched off, patterns are output in a simpler consensus pattern style (for instance Cxx--[DE] where x matches exactly one arbitrary sequence symbol and - matches zero or one arbitrary sequence symbol).
Default value is: On [true]
Max Num Patterns
Maximum number of patterns (ON parameter) between 1 and 100.
Default value is: 50
Max Num Alignments
Maximum number of alignments (OA parameter) between 1 and 100.
Default value is: 50
Print Patterns
Print Patterns in sequences (M parameter) If the M option is set, then Pratt will print out the location of the sequence segments matching each of the (maximum 52) best patterns. The patterns are given labels A, B,...Z,a,b,...z in order of decreasing pattern score. Each sequence is printed on a line, one character per K-tuple in the sequence. If pattern with label C matches the third K-tuple in a sequence C is printed out. If several patterns match in the same K-tuple, only the best will be printed.
Default value is: On [true]
Printing Ratio
Printing ratio (MR parameter). sets the K value (ratio) used for printing the summary information about where in each sequence the pattern matches are found.
Default value is: 10
Print Vertically
Print vertically (MV parameter). if set, the output is printed vertically instead of horizontally, vertical output can be better for large sequence sets.
Default value is: Off [false]
Step 3 - Submission
Job title
It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.
Email Notification
Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.
Email Address
If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).
Web Services
Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines.
For an introduction on how to run these clients and use them in workflows please see the webinar series.
REST API
The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
| Language | Download | Requirements |
|---|---|---|
| Perl | pratt.pl | LWP and XML::Simple |
Python | xmltramp2 |
For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.
WADL
The WADL for the Pratt (REST) service: http://www.ebi.ac.uk/Tools/services/rest/pratt?wadl
SOAP API
The Simple Object Access Protocol (SOAP) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
WSDL
The WSDL for the Pratt (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/pratt?wsdl
Open API Interface
https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=pratt
Common Workflow Language
CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl
For details, see CWL Workflows page.