
                                  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 
Nucleic acid pattern search
Input sequence(s): tembl:hhtetra
Search pattern: AAGCTT
Number of mismatches [0]: 
Output report [hhtetra.fuzznuc]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (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     Output report file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -complement         boolean    Search complementary strand

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated qualifiers
   -rformat2            string     Report format
   -rname2              string     Base file name
   -rextension2         string     File name extension
   -rdirectory2         string     Output directory
   -raccshow2           boolean    Show accession number in the report
   -rdesshow2           boolean    Show description in the report
   -rscoreshow2         boolean    Show the score in the report
   -rusashow2           boolean    Show the full USA in the report

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


   Standard (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) Output report file name Report output file
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -complement Search complementary strand Boolean value Yes/No No

Input file format

   fuzznuc reads in normal nucleic acid sequence USAs.

  Input files for usage example

   'tembl:hhtetra' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:hhtetra

ID   HHTETRA    standard; DNA; VRL; 1272 BP.
XX
AC   L46634; L46689;
XX
SV   L46634.1
XX
DT   06-NOV-1995 (Rel. 45, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 3)
XX
DE   Human herpesvirus 7 (clone ED132'1.2) telomeric repeat region.
XX
KW   telomeric repeat.
XX
OS   Human herpesvirus 7
OC   Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae.
XX
RN   [1]
RP   1-1272
RX   MEDLINE; 96079055.
RA   Secchiero P., Nicholas J., Deng H., Xiaopeng T., van Loon N., Ruvolo V.R.,
RA   Berneman Z.N., Reitz M.S. Jr., Dewhurst S.;
RT   "Identification of human telomeric repeat motifs at the genome termini of
RT   human herpesvirus 7: structural analysis and heterogeneity";
RL   J. Virol. 69(12):8041-8045(1995).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1272
FT                   /db_xref="taxon:10372"
FT                   /organism="Human herpesvirus 7"
FT                   /strain="JI"
FT                   /clone="ED132'1.2"
FT   repeat_region   207..928
FT                   /note="long and complex repeat region composed of various
FT                   direct repeats, including TAACCC (TRS), degenerate copies
FT                   of TRS motifs and a 14-bp repeat, TAGGGCTGCGGCCC"
FT   misc_signal     938..998
FT                   /note="pac2 motif"
FT   misc_feature    1009
FT                   /note="right genome terminus (...ACA)"
XX
SQ   Sequence 1272 BP; 346 A; 455 C; 222 G; 249 T; 0 other;
     aagcttaaac tgaggtcaca cacgacttta attacggcaa cgcaacagct gtaagctgca        6
0
     ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc       12
0
     tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa       18
0
     ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca       24
0
     actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc       30
0
     taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc       36
0
     taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc       42
0
     tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac       48
0
     cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc       54
0
     taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg       60
0
     gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc       66
0
     ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg       72
0
     cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac       78
0
     cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta       84
0
     accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta       90
0
     accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc       96
0
     cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac      102
0
     gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt      108
0
     agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga      114
0
     aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca      120
0
     agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa      126
0
     gttttcaagc tt                                                          127
2
//

  Pattern specification

   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).
     * All other characters, including spaces are not allowed.

   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://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default fuzznuc writes a 'seqtable' report file.

  Output files for usage example

  File: hhtetra.fuzznuc

########################################
# Program: fuzznuc
# Rundate: Thu Jul 15 2004 12:00:00
# Report_format: seqtable
# Report_file: hhtetra.fuzznuc
########################################

#=======================================
#
# 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)

   Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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

   None
