EMBOSS: preg

Program 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): sw:*_rat
Output file [100k_rat.preg]: stdout
Regular expression pattern: IA[QWF]A

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                bool       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

Output file format

preg search of sw:*_rat with pattern IA[QWF]A
Matches in 100K_RAT
       100K_RAT   390 IAQA
Matches in 5H6_RAT
        5H6_RAT   289 IAQA
Matches in ACDS_RAT
       ACDS_RAT   282 IAQA
Matches in ANX2_RAT
       ANX2_RAT    70 IAFA
Matches in APB3_RAT
       APB3_RAT   336 IAQA
Matches in AQP9_RAT
       AQP9_RAT    44 IAQA
Matches in ATHA_RAT
       ATHA_RAT   122 IAFA
Matches in CD14_RAT
       CD14_RAT   178 IAQA
Matches in CIKE_RAT
       CIKE_RAT   231 IAFA
Matches in CLCB_RAT
       CLCB_RAT    90 IAQA
Matches in CTR1_RAT
       CTR1_RAT   590 IAFA
Matches in CYGF_RAT
       CYGF_RAT   359 IAQA
Matches in DPY2_RAT
       DPY2_RAT   264 IAQA
Matches in ENOB_RAT
       ENOB_RAT   327 IAQA
Matches in ERBP_RAT
       ERBP_RAT    40 IAFA
Matches in GLPK_RAT
       GLPK_RAT   392 IAFA
Matches in GPV_RAT
        GPV_RAT   529 IAQA
Matches in IRKB_RAT
       IRKB_RAT    93 IAFA
Matches in KGP2_RAT
       KGP2_RAT   477 IAFA
Matches in NPX1_RAT
       NPX1_RAT   407 IAWA
Matches in NTDO_RAT
       NTDO_RAT   160 IAWA
Matches in NTSE_RAT
       NTSE_RAT   180 IAWA
Matches in PAX8_RAT
       PAX8_RAT   188 IAQA
Matches in SRA4_RAT
       SRA4_RAT   491 IAWA
Matches in SYNP_RAT
       SYNP_RAT    43 IAFA
Matches in TGN3_RAT
       TGN3_RAT   330 IAFA
Matches in TGR3_RAT
       TGR3_RAT   792 IAFA
Matches in UDB2_RAT
       UDB2_RAT   325 IAWA
Matches in UDB3_RAT
       UDB3_RAT   325 IAWA
Matches in UDB6_RAT
       UDB6_RAT   325 IAWA
Matches in UDBC_RAT
       UDBC_RAT   325 IAWA
Matches in VMT2_RAT
       VMT2_RAT   462 IAFA

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