| 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        60
         ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc       120
         tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa       180
         ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca       240
         actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc       300
         taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc       360
         taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc       420
         tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac       480
         cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc       540
         taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg       600
         gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc       660
         ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg       720
         cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac       780
         cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta       840
         accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta       900
         accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc       960
         cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac      1020
         gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt      1080
         agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga      1140
         aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca      1200
         agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa      1260
         gttttcaagc tt                                                          1272
    //

### 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