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

# wordfinder(1e)

Match large sequences against one or more other sequences

## NAME

wordfinder - Match large sequences against one or more other sequences

## SYNOPSIS

**wordfinder** **-asequence** *seqset* **-bsequence** *seqall* \[**-datafile** *matrixf*\] **-gapopen** *float* **-gapextend** *float* \[**-width** *integer*\] \[**-wordlen** *integer*\] \[**-limitmatch** *integer*\] \[**-limitalign** *integer*\] \[**-lowmatch** *integer*\] \[**-lowalign** *integer*\] **-outfile** *align* \[**-errorfile** *outfile*\]

**wordfinder** **-help**

## DESCRIPTION

**wordfinder** is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Alignment:Local" command group(s).

## OPTIONS

### Input section

- **-asequence** *seqset*

  - **-bsequence** *seqall*

  - **-datafile** *matrixf*

  This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.

### Required section

- **-gapopen** *float*

  Default value: @($(acdprotein)? 30.0 : 30.0)

- **-gapextend** *float*

  Default value: @($(acdprotein)? 1.5 : 1.5)

### Additional section

- **-width** *integer*

  Default value: 16

- **-wordlen** *integer*

  Default value: 6

- **-limitmatch** *integer*

  - **-limitalign** *integer*

  - **-lowmatch** *integer*

  - **-lowalign** *integer*

  ### Output section

- **-outfile** *align*

  - **-errorfile** *outfile*

  Error file to be written to Default value: wordfinder.error

## 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

wordfinder 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.