| FUZZNUC(1e) | EMBOSS Manual for Debian | FUZZNUC(1e) |
NAME¶
fuzznuc - Search for patterns in nucleotide sequencesSYNOPSIS¶
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 patternThe 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 booleanDefault value: N
Output section¶
-outfile reportBUGS¶
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.| 05/11/2012 | EMBOSS 6.4.0 |