EMBOSS: preg

Program preg

Function

regular expression search of a protein sequence

Description

This searches for matches of a regular expression to a protein sequence.

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

Here is a sample session with preg.


% preg
Input sequence: sw:*
Output file [5h1d_fugru.preg]: 
Regular expression pattern: gc[^g]

Command line arguments

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

   Optional qualifiers: (none)
   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

[-sequence]
(Parameter 1) Sequence database USA Readable sequence(s) Required

[-outfile]
(Parameter 2) Output file name Output file <sequence>.preg

[-pattern]
(Parameter 3) Regular expression pattern Any regular epression pattern is accepted Required

Optional qualifiers Allowed values Default

(none)

Advanced qualifiers Allowed values Default

(none)

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

Input file format

Any protein sequence.

Output file format

Here is the output from the example run:


Matches in CO9_FUGRU
      CO9_FUGRU   522 GCQ
Matches in D1DR_FUGRU
     D1DR_FUGRU    27 GCF
     D1DR_FUGRU   345 GCH
Matches in D5DR_FUGRU
     D5DR_FUGRU    43 GCV
     D5DR_FUGRU   349 GCS
Matches in HD_FUGRU
       HD_FUGRU   982 GCC
Matches in SYH_FUGRU
      SYH_FUGRU    15 GCR
Matches in SYV_FUGRU
      SYV_FUGRU   329 GCD
      SYV_FUGRU  1128 GCA
Matches in TCPD_FUGRU
     TCPD_FUGRU   291 GCN
     TCPD_FUGRU   375 GCA
Matches in ACH2_DROME
     ACH2_DROME     4 GCC
     ACH2_DROME   433 GCN
Matches in LACY_ECOLI
     LACY_ECOLI   147 GCV
     LACY_ECOLI   175 GCA
     LACY_ECOLI   332 GCF
Matches in BGAL_ECOLI
     BGAL_ECOLI   121 GCY
Matches in 12S1_ARATH
     12S1_ARATH   111 GCA
Matches in OPSD_HUMAN
     OPSD_HUMAN   109 GCN
Matches in AMIC_PSEAE
     AMIC_PSEAE    80 GCY
Matches in AMIR_PSEAE
     AMIR_PSEAE    36 GCS

Data files

Notes

References

Warnings

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

Diagnostic Error Messages

Exit status

Always returns 0.

Known bugs

Program name	Description
dreg	regular expression search of a nucleotide sequence
fuzznuc	Nucleic acid pattern search
fuzzpro	Protein pattern search
fuzztran	Protein pattern search after translation
patmatdb	Search a protein sequence with a motif
patmatmotifs	Search a PROSITE motif database with a protein sequence
pscan	Scans proteins using PRINTS
tfscan	Scans DNA sequences for transcription factors

Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.