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<HTML>
<HEAD>
<TITLE>
EMBOSS: fuzznuc
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
fuzznuc
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Nucleic acid pattern search
<H2>
Description
</H2>
fuzznuc uses PROSITE style patterns to search nucleotide sequences.
<p>
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.
<p>
fuzznuc intelligently selects the optimum searching algorithm to use,
depending on the complexity of the search pattern specified.
<H2>
Usage
</H2>
<b>Here is a sample session with fuzznuc</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>fuzznuc </b>
Nucleic acid pattern search
Input nucleotide sequence(s): <b>tembl:L46634</b>
Search pattern: <b>AAGCTT</b>
Output report [l46634.fuzznuc]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>fuzznuc </b>
Nucleic acid pattern search
Input nucleotide sequence(s): <b>tembl:L46634</b>
Search pattern: <b>@nucseq.pat</b>
Output report [l46634.fuzznuc]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.2">Go to the input files for this example</a><br><a href="#output.2">Go to the output files for this example</a><p><p>
<p>
<b>Example 3</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>fuzznuc -pname test </b>
Nucleic acid pattern search
Input nucleotide sequence(s): <b>tembl:L46634</b>
Search pattern: <b>@nucsimple.pat</b>
Output report [l46634.fuzznuc]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.3">Go to the input files for this example</a><br><a href="#output.3">Go to the output files for this example</a><p><p>
<p>
<b>Example 4</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>fuzznuc </b>
Nucleic acid pattern search
Input nucleotide sequence(s): <b>tembl:L46634</b>
Search pattern: <b>@nuc.pat</b>
Output report [l46634.fuzznuc]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.4">Go to the input files for this example</a><br><a href="#output.4">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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
-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 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 dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-pattern</td>
<td>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</td>
<td>Property value(s)</td>
<td> </td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i><*></i>.fuzznuc</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-complement</td>
<td>Search complementary strand</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>fuzznuc</b> reads in normal nucleic acid sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:L46634' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:L46634</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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 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
//
</pre>
</td></tr></table><p>
<a name="input.2"></a>
<h3>Input files for usage example 2</h3>
<p><h3>File: nucseq.pat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
>targetseq
cg(2)c(3)taac
cctagc(3)ta
</pre>
</td></tr></table><p>
<a name="input.3"></a>
<h3>Input files for usage example 3</h3>
<p><h3>File: nucsimple.pat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
cg(2)c(3)taac
cctagc(3)ta
</pre>
</td></tr></table><p>
<a name="input.4"></a>
<h3>Input files for usage example 4</h3>
<p><h3>File: nuc.pat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
>pat1
cggccctaaccctagcccta
>pat2 <mismatch=1>
cg(2)c(3)taac
cctagc(3)ta
>pat3
cggc(2,4)taac(2,5)
</pre>
</td></tr></table><p>
<h3>Pattern specification</h3>
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.
<p>
The PROSITE pattern definition from the PROSITE documentation (amended
to refer to nucleic acid sequences, not proteins) follows.
<ul>
<li>The standard IUPAC one-letter codes for the nucleotides are used.
<li>The symbol `n' is used for a position where any nucleotide is
accepted.
<li>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.
<li>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.
<li>Each element in a pattern is separated from its neighbor by a `-'.
(Optional in fuzznuc).
<li>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.
<li>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.
<li>A period ends the pattern. (Optional in fuzznuc).
<li>All other characters, including spaces are not allowed.
</ul>
<p>
For example, in the EMBL entry ECLAC you can look for the pattern:
<pre>
[CG](5)TG{A}N(1,5)C
</pre>
<p>
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.
<p>
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.
<p>
Note the use of X is reserved for proteins. You must use N for nucleic
acids to refer to any base.
<p>
The search is case-independent, so 'AAA' matches 'aaa'.
<H2>
Output file format
</H2>
<p>
The output is a standard EMBOSS report file.
<p>
The results can be output in one of several styles by using the
command-line qualifier <b>-rformat xxx</b>, 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
<p>
See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.
<p>
<p>
By default <b>fuzznuc</b> writes a 'seqtable' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: l46634.fuzznuc</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: fuzznuc
# Rundate: Sun 15 Jul 2007 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 Pattern_name Mismatch Sequence
1 6 pattern1 . aagctt
1267 1272 pattern1 . aagctt
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 2
#---------------------------------------
</pre>
</td></tr></table><p>
<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: l46634.fuzznuc</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: fuzznuc
# Rundate: Sun 15 Jul 2007 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 Pattern_name Mismatch Sequence
429 448 targetseq . cggccctaaccctagcccta
491 510 targetseq . cggccctaaccctagcccta
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 2
#---------------------------------------
</pre>
</td></tr></table><p>
<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: l46634.fuzznuc</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: fuzznuc
# Rundate: Sun 15 Jul 2007 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 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
#---------------------------------------
</pre>
</td></tr></table><p>
<a name="output.4"></a>
<h3>Output files for usage example 4</h3>
<p><h3>File: l46634.fuzznuc</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: fuzznuc
# Rundate: Sun 15 Jul 2007 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 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
#---------------------------------------
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with a status of 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="dreg.html">dreg</a></td>
<td>Regular expression search of a nucleotide sequence</td>
</tr>
<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>Protein pattern search after translation</td>
</tr>
<tr>
<td><a href="marscan.html">marscan</a></td>
<td>Finds MAR/SAR sites in nucleic sequences</td>
</tr>
</table>
<p>
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:
<p>
<ul>
<li><a href="dreg.html">dreg</a> - Regular expression search of a
nucleotide sequence
<li><a href="preg.html">preg</a> - Regular expression search of a protein
sequence
</ul>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written (2000) - Alan Bleasby
<br>
'-usa' added (13 March 2001) - Gary Williams
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
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