
                              EMBOSS: fuzznuc
     _________________________________________________________________
   
                                Program fuzznuc
                                       
Function

   Nucleic acid pattern search
   
Description

   fuzznuc uses PROSITE style patterns to search nucleotide sequences.
   
   Patterns are specifications of a (typically short) length of sequence
   to be found. They can specify a search for an exact sequence or they
   can allow various ambiguities, matches to variable lengths of sequence
   and repeated subsections of the sequence.
   
   fuzznuc intelligently selects the optimum searching algorithm to use,
   depending on the complexity of the search pattern specified.
   
Usage

   Here is a sample session with fuzznuc.

% fuzznuc
Input sequence: embl:hhtetra
Search pattern: AAGCTT
Number of mismatches [0]:
Output file [hhtetra.fuzznuc]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -pattern            string     The standard IUPAC one-letter codes for the
                                  nucleotides are used.
                                  The symbol `n' is used for a position where
                                  any nucleotide is accepted.
                                  Ambiguities are indicated by listing the
                                  acceptable nucleotides for a given position,
                                  between square parentheses `[ ]'. For
                                  example: [ACG] stands for A or C or G.
                                  Ambiguities are also indicated by listing
                                  between a pair of curly brackets `{ }' the
                                  nucleotides that are not accepted at a given
                                  position. For example: {AG} stands for any
                                  nucleotides except A and G.
                                  Each element in a pattern is separated from
                                  its neighbor by a `-'. (Optional in
                                  fuzznuc).
                                  Repetition of an element of the pattern can
                                  be indicated by following that element with
                                  a numerical value or a numerical range
                                  between parenthesis. Examples: N(3)
                                  corresponds to N-N-N, N(2,4) corresponds to
                                  N-N or N-N-N or N-N-N-N.
                                  When a pattern is restricted to either the
                                  5' or 3' end of a sequence, that pattern
                                  either starts with a `<' symbol or
                                  respectively ends with a `>' symbol.
                                  A period ends the pattern. (Optional in
                                  fuzznuc).
                                  For example, [CG](5)TG{A}N(1,5)C
   -mismatch           integer    Number of mismatches
  [-outfile]           report     (no help text) report value

   Optional qualifiers: (none)
   Advanced qualifiers:
   -complement         bool       Search complementary strand

   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 The standard IUPAC one-letter codes for the nucleotides are
   used. The symbol `n' is used for a position where any nucleotide is
   accepted. Ambiguities are indicated by listing the acceptable
   nucleotides for a given position, between square parentheses `[ ]'.
   For example: [ACG] stands for A or C or G. Ambiguities are also
   indicated by listing between a pair of curly brackets `{ }' the
   nucleotides that are not accepted at a given position. For example:
   {AG} stands for any nucleotides except A and G. Each element in a
   pattern is separated from its neighbor by a `-'. (Optional in
   fuzznuc). Repetition of an element of the pattern can be indicated by
   following that element with a numerical value or a numerical range
   between parenthesis. Examples: N(3) corresponds to N-N-N, N(2,4)
   corresponds to N-N or N-N-N or N-N-N-N. When a pattern is restricted
   to either the 5' or 3' end of a sequence, that pattern either starts
   with a `<' symbol or respectively ends with a `>' symbol. A period
   ends the pattern. (Optional in fuzznuc). For example,
   [CG](5)TG{A}N(1,5)C Any string is accepted An empty string is accepted
   -mismatch Number of mismatches Integer 0 or more 0
   [-outfile]
   (Parameter 2) (no help text) report value Report file
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -complement Search complementary strand Yes/No No
   
Input file format

   Patterns for fuzznuc are based on the format of pattern used in the
   PROSITE database, with the difference that the terminating dot '.' and
   the hyphens, '-', between the characters are optional.
   
   The PROSITE pattern definition from the PROSITE documentation (amended
   to refer to nucleic acid sequences, not proteins) follows.
     * The standard IUPAC one-letter codes for the nucleotides are used.
     * The symbol `n' is used for a position where any nucleotide is
       accepted.
     * Ambiguities are indicated by listing the acceptable nucleotides
       for a given position, between square parentheses `[ ]'. For
       example: [ACG] stands for A or C or G.
     * Ambiguities are also indicated by listing between a pair of curly
       brackets `{ }' the nucleotides that are not accepted at a given
       position. For example: {AG} stands for any nucleotides except A
       and G.
     * Each element in a pattern is separated from its neighbor by a `-'.
       (Optional in fuzznuc).
     * Repetition of an element of the pattern can be indicated by
       following that element with a numerical value or a numerical range
       between parenthesis. Examples: N(3) corresponds to N-N-N, N(2,4)
       corresponds to N-N or N-N-N or N-N-N-N.
     * When a pattern is restricted to either the 5' or 3' end of a
       sequence, that pattern either starts with a `<' symbol or
       respectively ends with a `>' symbol.
     * A period ends the pattern. (Optional in fuzznuc).
       
   For example, in the EMBL entry ECLAC you can look for the pattern:

[CG](5)TG{A}N(1,5)C

   This searches for "C or G" 5 times, followed by T and G, then anything
   except A, then any base (1 to 5 times) before a C.
   
   You can use ambiguity codes for nucleic acid searches but not within
   [] or {} as they expand to bracketed counterparts. For example, "s" is
   expanded to "[GC]" therefore [S] would be expanded to [[GC]] which is
   illegal.
   
   Note the use of X is reserved for proteins. You must use N for nucleic
   acids to refer to any base.
   
   The search is case-independent, so 'AAA' matches 'aaa'.
   
Output file format

   The output is a standard EMBOSS report file.
   
   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq
   
   See:
   http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for
   further information on report formats.
   
   By default fuzznuc writes a 'seqtable' report file.
   
   The output from the above example is:
   
########################################
# Program: fuzznuc
# Rundate: Thu Apr 11 13:34:06 2002
# Report_file: stdout
########################################

#=======================================
#
# Sequence: HHTETRA     from: 1   to: 1272
# HitCount: 2
#
# Pattern: aagctt
# Mismatch: 0
# Complement: No
#
#=======================================

  Start     End Mismatch Sequence
      1       6        . aagctt
   1267    1272        . aagctt

#---------------------------------------
#---------------------------------------

Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name                    Description
   dreg         regular expression search of a nucleotide sequence
   fuzztran     Protein pattern search after translation
   marscan      Finds MAR/SAR sites in nucleic sequences
   
   Other EMBOSS programs allow you to search for regular expression
   patterns but may be less easy for the user who has never used regular
   expressions before:
   
     * dreg - Regular expression search of a nucleotide sequence
     * preg - Regular expression search of a protein sequence
       
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Written (2000) - Alan Bleasby
   '-usa' added (13 March 2001) - Gary Williams
   
Target users

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