
                                   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 
regular expression search of a nucleotide sequence
Input sequence(s): tembl:paamir
Regular expression pattern: ggtacc
Output file [paamir.dreg]: 
   
   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>.dreg
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Any nucleic sequence.
   
  Input files for usage example
  
   'tembl:paamir' is a sequence entry in the example nucleic acid
   database 'tembl'
   
  Database entry: tembl:paamir
  
ID   PAAMIR     standard; DNA; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
SV   X13776.1
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   17-FEB-1997 (Rel. 50, Last updated, Version 22)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas
.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
RN   [2]
RP   1167-2167
RX   MEDLINE; 89211409.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomona
s
RT   aeruginosa";
RL   FEBS Lett. 246:39-43(1989).
XX
RN   [3]
RP   1-1292
RX   MEDLINE; 91317707.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product.";
RL   J. Bacteriol. 173:4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
DR   SWISS-PROT; P10932; AMIR_PSEAE.
DR   SWISS-PROT; P27017; AMIC_PSEAE.
DR   SWISS-PROT; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

FT                   phenotype"
FT                   /replace=""
FT                   /gene="amiC"
FT   misc_feature    1
FT                   /note="last base of an XhoI site"
FT   misc_feature    648..653
FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 cause
s
FT                   constitutive expression of amiE"
FT   conflict        1281
FT                   /replace="g"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        6
0
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       12
0
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       18
0
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       24
0
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       30
0
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       36
0
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       42
0
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       48
0
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       54
0
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       60
0
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       66
0
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       72
0
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       78
0
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       84
0
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       90
0
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       96
0
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      102
0
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      108
0
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      114
0
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      120
0
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      126
0
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      132
0
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      138
0
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      144
0
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      150
0
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      156
0
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      162
0
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      168
0
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      174
0
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      180
0
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      186
0
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      192
0
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      198
0
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      204
0
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      210
0
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      216
0
     cctcgag                                                                216
7
//
   
Output file format

  Output files for usage example
  
  File: paamir.dreg
  
dreg search of tembl: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
