preg

Function

Description

A regular expression is a way of specifying an ambiguous pattern to search for. Regular expressions are commonly used in some computer programming languages and may be more familiar to some users than to others.

The following is a short guide to regular expressions in EMBOSS:

^

use this at the start of a pattern to insist that the pattern can only match at the start of a sequence. (eg. '^M' matches a methionine at the start of the sequence)

$

use this at the end of a pattern to insist that the pattern can only match at the end of a sequence (eg. 'R$' matches an arginine at the end of the sequence)

()

groups a pattern. This is commonly used with '|' (eg. '(ACD)|(VWY)' matches either the first 'ACD' or the second 'VWY' pattern )

|

This is the OR operator to enable a match to be made to either one pattern OR another. There is no AND operator in this version of regular expressions.

The following quantifier characters specify the number of time that the character before (in this case 'x') matches:

x?

matches 0 or 1 times (ie, '' or 'x')

x*

matches 0 or more times (ie, '' or 'x' or 'xx' or 'xxx', etc)

x+

matches 1 or more times (ie, 'x' or 'xx' or 'xxx', etc)

Quantifiers can follow any of the following types of character specification:

x

any character (ie 'A')

\x

the character after the backslash is used instead of its normal regular expression meaning. This is commonly used to turn off the special meaning of the characters '^$()|?*+[]-.'. It may be especially useful when searching for gap characters in a sequence (eg '\.' matches only a dot character '.')

[xy]

match one of the characters 'x' or 'y'. You may have one or more characters in this set.

[x-z]

match any one of the set of characters starting with 'x' and ending in 'y' in ASCII order (eg '[A-G]' matches any one of: 'A', 'B', 'C', 'D', 'E', 'F', 'G')

[^x-z]

matches anything except any one of the group of characters in ASCII order (eg '[^A-G]' matches anything EXCEPT any one of: 'A', 'B', 'C', 'D', 'E', 'F', 'G')

.

the dot character matches any other character (eg: 'A.G' matches 'AAG', 'AaG', 'AZG', 'A-G' 'A G', etc.)

Combining some of these features gives these examples from the PROSITE patterns database:

'[STAGCN][RKH][LIVMAFY]$'

which is the 'Microbodies C-terminal targeting signal'.

'LP.TG[STGAVDE]'

which is the 'Gram-positive cocci surface proteins anchoring hexapeptide'.

Regular expressions are case-sensitive. The pattern 'AAAA' will not match the sequence 'aaaa'.

Usage

% preg Regular expression search of a protein sequence Input sequence(s): tsw:*_rat Regular expression pattern: IA[QWF]A Output file [100k_rat.preg]:

Go to the input files for this example
Go to the output files for this example

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-pattern]           regexp     Regular expression pattern
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose

Mandatory qualifiers		Allowed values	Default
[-sequence] (Parameter 1)	Sequence database USA	Readable sequence(s)	Required
[-pattern] (Parameter 2)	Regular expression pattern	Any regular epression pattern is accepted	Required
[-outfile] (Parameter 3)	Output file name	Output file	<sequence>.preg
Optional qualifiers		Allowed values	Default
(none)
Advanced qualifiers		Allowed values	Default
(none)

Input file format

Input files for usage example

Output file format

Output files for usage example

File: 100k_rat.preg

preg search of tsw:*_rat with pattern IA[QWF]A
Matches in 100K_RAT
       100K_RAT   390 IAQA

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Other EMBOSS programs allow you to search for simple patterns and may be easier for the user who has never used regular expressions before:

• fuzznuc - Nucleic acid pattern search
• fuzzpro - Protein pattern search
• fuzztran - Protein pattern search after translation

Author(s)

History

Target users

Comments