fuzznuc - Search for patterns in nucleotide sequences
fuzznuc -sequence seqall
-pattern pattern
-complement boolean
-outfile report
fuzznuc -help
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).
-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
-complement boolean
Default value: N
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).
fuzznuc is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
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.