EMBOSS: dreg

| ## EMBOSS: dreg

# Program dreg

## Function

regular expression search of a nucleotide sequence

## Description

This searches for matches of a regular expression to a nucleic acid 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. '^AUG' matches a start codon 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. 'A+$' matches a poly-A sequence at the end of the sequence)
()
  groups a pattern. This is commonly used with '|' (eg. '(AUG)|(ATG)' matches either the DNA or RNA form of the initiation codon )
|
  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 the example:

    '([AGC]+GGG)|(TTTGGG)'

which matches one or more of any one of 'A' or 'G' or 'C' followed by three 'G's or it matches just 'TTTGGG'.

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

## Usage

Here is a sample session with dreg.

    % dreg
    Input sequence: embl:paamir
    Output file [paamir.dreg]:
    Regular expression pattern: ggtacc

## 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>.dreg
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Any nucleic sequence.

## Output file format

This is the output from the example run. Sequence embl:paamir begins at a restriction site with the sequence pattern GGTACC.

    dreg search of embl:paamir with pattern GGTACC
    Matches in PAAMIR
             PAAMIR     1 GGTACC

## Data files

None.

## Notes

None.

## References

None.

## Warnings

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

## Diagnostic Error Messages

None.

## Exit status

Always returns 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
fuzznuc | Nucleic acid pattern search
fuzztran | Protein pattern search after translation
marscan | Finds MAR/SAR sites in nucleic sequences

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)

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

Written (1999) - Peter Rice.

## Target users

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

## Comments