'\" t
.\"     Title: FUZZNUC
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\"      Date: 05/11/2012
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: EMBOSS 6.4.0
.\"  Language: English
.\"
.TH "FUZZNUC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.\" -----------------------------------------------------------------
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
fuzznuc \- Search for patterns in nucleotide sequences
.SH "SYNOPSIS"
.HP \w'\fBfuzznuc\fR\ 'u
\fBfuzznuc\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-complement\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
.HP \w'\fBfuzznuc\fR\ 'u
\fBfuzznuc\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBfuzznuc\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Motifs" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIseqall\fR
.RS 4
.RE
.PP
\fB\-pattern\fR \fIpattern\fR
.RS 4
The standard IUPAC one\-letter codes for the nucleotides are used\&. The symbol \*(Aqn\*(Aq 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 \*(Aq[ ]\*(Aq\&. For example: [ACG] stands for A or C or G\&. Ambiguities are also indicated by listing between a pair of curly brackets \*(Aq{ }\*(Aq 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 \*(Aq\-\*(Aq\&. (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\*(Aq or 3\*(Aq end of a sequence, that pattern either starts with a \*(Aq<\*(Aq symbol or respectively ends with a \*(Aq>\*(Aq symbol\&. A period ends the pattern\&. (Optional in fuzznuc)\&. For example, [CG](5)TG{A}N(1,5)C
.RE
.SS "Advanced section"
.PP
\fB\-complement\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIreport\fR
.RS 4
.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
.SH "SEE ALSO"
.PP
fuzznuc is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
.sp