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Table 1 Common regular expressions and the n-of-m pattern type in the 3of5 application Individual common RegEx terms are displayed as they can be applied in 3of5. Types of allowed ambiguities in the individual RegEx terms are listed. "no" no ambiguity; "yes" ambiguity can be expressed with that particular term; "any" ambiguity with any residue allowed. Notes: (1) The general term "ambiguity" used in the text is extended here to "content-ambiguity" to distinguish this from the "length ambiguity"

From: The 3of5 web application for complex and comprehensive pattern matching in protein sequences

Different levels of Regex descriptions

Verbal description

Example of syntax

Potentially content-ambiguous(1)

Potentially length-ambiguous

Description of single positions

Discrete character in one position

K

no

no

 

Subset of characters for one position

[KRH]

yes

no

 

Arbitrary character in one position

.

any

no

Description of multiple positions

Stretch of identical characters, with fixed length

K {3}

no

no

 

Stretch composed of a subset of characters, with fixed length

[KRH] {3}

yes

no

 

Stretch of identical characters, with variable length

K {1,3}

no

yes

 

Stretch composed of a subset of characters, with variable length

[KRH] {1,3}

yes

yes

 

Stretch with arbitrary characters, with variable length

. {1,3}

any

yes

Description of multiple positions of n-of-m

Stretch composed of a subset of characters that need to be present with a defined number of matches within sequence of otherwise arbitrary composition, with fixed length

(3of5) (KRH)

yes

no

Description of multiple positions of n-of-m in extended syntax

Stretch composed of different subsets of characters that need to be present with defined numbers of matches within sequence of otherwise arbitrary composition, with fixed length

(nof5) ((min3) (KRH) (max1) (P))

yes

no

Restriction of content of single/multiple positions

Any stretch describable by a pattern which should not contain the characters defined in the [^ ] brackets

[AGC] {2,5} [^KRH]

no

no

Restriction of position of total pattern

Pattern begins at sequence start

^ KKK

no

no

 

Pattern ends at sequence end

KKK $

no

no