PRATT

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PRATT

PRATT is a tool to discover patterns conserved in a set of protein sequences.

This tool can also be run from the EBI server with very similar modalities.

STEP 1 - Enter a set of PROTEIN sequences or an alignment

Supported input:

Sequences in FASTA or UniProtKB/Swiss-Prot format
Alignment of sequences in FASTA format

Your input is a set of sequences an alignment

Option in command line format: -G
If 'alignment' is chosen, then the input is considered as an alignment which will be used to guide the pattern search and only patterns consistent with it will be considered by PRATT.
Loosely, a pattern is considered consistent with the alignment if each symbol in the pattern corresponds to an ungapped column in the alignment and all the characters of the column in question match the pattern symbol. Also, the wildcards in the pattern must be compatible with the number of residues between the corresponding columns in the alignment.
For instance, the pattern

A-x(2,3)-B

is consistent with the following alignment:

    ALVGB
    AG-LB
    ALD-B

STEP 2 - Modify default parameters (optional) » Pattern parameters

The pattern must match at least

Max pattern length

Option in command line format: -PL
Set the maximum length of a pattern for PRATT to consider it.
For instance,

G-G-[PS]-L-x(1,3)-R

has a length of 8 (1+1+1+1+3+1).

Max number of different pattern symbols

Option in command line format: -PN
Set the maximum number of different symbols in a pattern for PRATT to consider it.
For instance,

G-G-[PS]-L-x(1,3)-R

has 4 different symbols:

G, [PS], L and R

Max length of wildcards (x)

Option in command line format: -PX
Set the maximum length of every wildcard (x) in a pattern for PRATT to consider it.
For instance

has a length of 1,

x(7)

has a length of 7 and

x(1,3)

has a length of 3.

Max number of flexible wildcards (x)

Option in command line format: -FN
Set the maximum number of flexible wildcards (x) in a pattern for PRATT to consider it.
For instance,

A-x(2)-P-x-G-x(0,2)-D-x(3,5)-S

contains 2 flexible wildcards:

x(0,2)

and

x(3,5)

Max flexibility of wildcards (x)

Option in command line format: -FL
Set the maximum flexibility of every wildcard in a pattern for PRATT to consider it.
For instance,

x(3)

has a flexibility of 0,

x(1,2)

has a flexibility of 1 and

x(0,2)

has a flexibility of 2.

Max product of wildcard (x) flexibility

Option in command line format: -FP
Set the maximum product of all wildcard flexibility of a pattern for PRATT to consider it.
The equation for calculating the product is:

(flexibility of wildcard_1 + 1) * ... * (flexibility of wildcard_n + 1)

For instance, for

C-x(2,4)-[DE]-x(10)-F

the product is

(2+1) * (0+1)

= 3
and for

C-x(2,4)-[DE]-x(10,14)-F

the product is

(2+1) * (4+1)

= 15.

Maximum number of pattern symbols used in the initial search

Option in command line format: -BN
PRATT uses a set of pattern symbols to perform the search. This set contains the 20 one-letter amino acid symbols like

followed by ambiguous symbols of amino acids sharing some physico-chemical properties like

[DE]

.
With this option, you can choose the maximum number of pattern symbols that will be used during the initial search.

Pattern scoring method

» Search parameters
» Output parameters

Pattern format

Max number of patterns

Max number of alignments

Print patterns in sequences

Ratio for printing

Print vertically

If you're familiar with PRATT, you can directly enter parameters in a command line format:

e.g. -PL 25

STEP 3 - Submit your job Directly submit best pattern to ScanProsite
View PRATT output file

Tool By :SIB Swiss Institute of Bioinformatics | Disclaimer

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