
                                  fuzznuc 



Function

   Search for patterns in nucleotide sequences

Description

   fuzznuc searches for a specified PROSITE-style pattern in nucleotide
   sequences. Such 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. One or
   more nucleotide sequences are read from file. The output is a standard
   EMBOSS report file that includes data such as location and score of
   any matches.

Algorithm

   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 
Search for patterns in nucleotide sequences
Input nucleotide sequence(s): tembl:L46634
Search pattern: AAGCTT
Output report [l46634.fuzznuc]: 

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

   Example 2


% fuzznuc 
Search for patterns in nucleotide sequences
Input nucleotide sequence(s): tembl:L46634
Search pattern: @nucseq.pat
Output report [l46634.fuzznuc]: 

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

   Example 3


% fuzznuc -pname test 
Search for patterns in nucleotide sequences
Input nucleotide sequence(s): tembl:L46634
Search pattern: @nucsimple.pat
Output report [l46634.fuzznuc]: 

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

   Example 4


% fuzznuc 
Search for patterns in nucleotide sequences
Input nucleotide sequence(s): tembl:L46634
Search pattern: @nuc.pat
Output report [l46634.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     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -pattern            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
  [-outfile]           report     [*.fuzznuc] Output report file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -complement         boolean    [N] 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

   "-pattern" associated qualifiers
   -pformat            string     File format
   -pmismatch          integer    Pattern mismatch
   -pname              string     Pattern base 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
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 dying program messages

Input file format

   fuzznuc reads in normal nucleic acid sequence USAs.

  Input files for usage example

   'tembl:L46634' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:L46634

ID   L46634; SV 1; linear; genomic DNA; STD; VRL; 1272 BP.
XX
AC   L46634; L46689;
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;
OC   Roseolovirus.
XX
RN   [1]
RP   1-1272
RX   PUBMED; 7494318.
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                   /organism="Human herpesvirus 7"
FT                   /strain="JI"
FT                   /mol_type="genomic DNA"
FT                   /clone="ED132'1.2"
FT                   /db_xref="taxon:10372"
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
//

  Input files for usage example 2

  File: nucseq.pat

>targetseq
cg(2)c(3)taac
cctagc(3)ta

  Input files for usage example 3

  File: nucsimple.pat

cg(2)c(3)taac
cctagc(3)ta

  Input files for usage example 4

  File: nuc.pat

>pat1
cggccctaaccctagcccta
>pat2 <mismatch=1>
cg(2)c(3)taac
cctagc(3)ta
>pat3
cggc(2,4)taac(2,5)

  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 J01636 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: l46634.fuzznuc

########################################
# Program: fuzznuc
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: fuzznuc
#    -sequence tembl:L46634
#    -pattern AAGCTT
# Report_format: seqtable
# Report_file: l46634.fuzznuc
########################################

#=======================================
#
# Sequence: L46634     from: 1   to: 1272
# HitCount: 2
#
# Pattern_name Mismatch Pattern
# pattern1            0 AAGCTT
#
# Complement: No
#
#=======================================

  Start     End  Strand Pattern_name Mismatch Sequence
      1       6       + pattern1            . aagctt
   1267    1272       + pattern1            . aagctt

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

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 2
#---------------------------------------

  Output files for usage example 2

  File: l46634.fuzznuc

########################################
# Program: fuzznuc
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: fuzznuc
#    -sequence tembl:L46634
#    -pattern @../../data/nucseq.pat
# Report_format: seqtable
# Report_file: l46634.fuzznuc
########################################

#=======================================
#
# Sequence: L46634     from: 1   to: 1272
# HitCount: 2
#
# Pattern_name Mismatch Pattern
# targetseq           0 cg(2)c(3)taaccctagc(3)ta
#
# Complement: No
#
#=======================================

  Start     End  Strand Pattern_name Mismatch Sequence
    429     448       + targetseq           . cggccctaaccctagcccta
    491     510       + targetseq           . cggccctaaccctagcccta

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

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 2
#---------------------------------------

  Output files for usage example 3

  File: l46634.fuzznuc

########################################
# Program: fuzznuc
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: fuzznuc
#    -pname test
#    -sequence tembl:L46634
#    -pattern @../../data/nucsimple.pat
# Report_format: seqtable
# Report_file: l46634.fuzznuc
########################################

#=======================================
#
# Sequence: L46634     from: 1   to: 1272
# HitCount: 13
#
# Pattern_name Mismatch Pattern
# test1               0 cg(2)c(3)taac
# test2               0 cctagc(3)ta
#
# Complement: No
#
#=======================================

  Start     End  Strand Pattern_name Mismatch Sequence
    429     438       + test1               . cggccctaac
    491     500       + test1               . cggccctaac
    535     544       + test1               . cggccctaac
    605     614       + test1               . cggccctaac
    631     640       + test1               . cggccctaac
    695     704       + test1               . cggccctaac
    721     730       + test1               . cggccctaac
    753     762       + test1               . cggccctaac
    293     302       + test2               . cctagcccta
    439     448       + test2               . cctagcccta
    469     478       + test2               . cctagcccta
    501     510       + test2               . cctagcccta
    801     810       + test2               . cctagcccta

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

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 13
#---------------------------------------

  Output files for usage example 4

  File: l46634.fuzznuc

########################################
# Program: fuzznuc
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: fuzznuc
#    -sequence tembl:L46634
#    -pattern @../../data/nuc.pat
# Report_format: seqtable
# Report_file: l46634.fuzznuc
########################################

#=======================================
#
# Sequence: L46634     from: 1   to: 1272
# HitCount: 19
#
# Pattern_name Mismatch Pattern
# pat1                0 cggccctaaccctagcccta
# pat2                1 cg(2)c(3)taaccctagc(3)ta
# pat3                0 cggc(2,4)taac(2,5)
#
# Complement: No
#
#=======================================

  Start     End  Strand Pattern_name Mismatch Sequence
    429     448       + pat1                . cggccctaaccctagcccta
    491     510       + pat1                . cggccctaaccctagcccta
    429     448       + pat2                . cggccctaaccctagcccta
    491     510       + pat2                . cggccctaaccctagcccta
    535     554       + pat2                1 cggccctaaccctaacccta
    605     624       + pat2                1 cggccctaaccctaacccta
    631     650       + pat2                1 cggccctaaccctaacccta
    695     714       + pat2                1 cggccctaaccctaacccta
    721     740       + pat2                1 cggccctaaccctaacccta
    753     772       + pat2                1 cggccctaaccctaacccta
    791     810       + pat2                1 cggcccgaaccctagcccta
    753     764       + pat3                . cggccctaaccc
    721     732       + pat3                . cggccctaaccc
    695     706       + pat3                . cggccctaaccc
    631     642       + pat3                . cggccctaaccc
    605     616       + pat3                . cggccctaaccc
    535     546       + pat3                . cggccctaaccc
    491     502       + pat3                . cggccctaaccc
    429     440       + pat3                . cggccctaaccc

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

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 19
#---------------------------------------

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 nucleotide sequence(s)
   fuzztran Search for patterns in protein sequences (translated)
   marscan Finds matrix/scaffold recognition (MRS) signatures in DNA
   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 (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, 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
