---
name: "fuzznuc"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fuzznuc"
---

# fuzznuc(1e)

Search for patterns in nucleotide sequences

## 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)](/N/3.md) 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.