NAME

       fuzznuc - Search for patterns in nucleotide sequences

SYNOPSIS

       fuzznuc -sequence seqall -pattern pattern -complement boolean -outfile report

       fuzznuc -help

DESCRIPTION

       fuzznuc is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It
       is part of the "Nucleic:Motifs" command group(s).

OPTIONS

   Input section
       -sequence seqall

       -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

   Advanced section
       -complement boolean
           Default value: N

   Output section
       -outfile report

BUGS

       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).

SEE ALSO

       fuzznuc is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       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.

EMBOSS 6.4.0                                       05/11/2012                                        FUZZNUC(1e)