Pratt

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 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 be in FASTA or UniProtKB/Swiss-Prot format. A partially formatted sequences are not accepted. 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. 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).

References

Finding flexible patterns in unaligned protein sequences.
(1995 Aug) Protein science : a publication of the Protein Society 4 (8) :1587-95
Efficient discovery of conserved patterns using a pattern graph.
(1997 Oct) Computer applications in the biosciences : CABIOS 13 (5) :509-22
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600