'\" t
.\"     Title: WORDFINDER
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\"      Date: 05/11/2012
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: EMBOSS 6.4.0
.\"  Language: English
.\"
.TH "WORDFINDER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.SH "NAME"
wordfinder \- Match large sequences against one or more other sequences
.SH "SYNOPSIS"
.HP \w'\fBwordfinder\fR\ 'u
\fBwordfinder\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-width\ \fR\fB\fIinteger\fR\fR] [\fB\-wordlen\ \fR\fB\fIinteger\fR\fR] [\fB\-limitmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-limitalign\ \fR\fB\fIinteger\fR\fR] [\fB\-lowmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-lowalign\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR]
.HP \w'\fBwordfinder\fR\ 'u
\fBwordfinder\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBwordfinder\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-asequence\fR \fIseqset\fR
.RS 4
.RE
.PP
\fB\-bsequence\fR \fIseqall\fR
.RS 4
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
.RS 4
This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
.RE
.SS "Required section"
.PP
\fB\-gapopen\fR \fIfloat\fR
.RS 4
Default value: @($(acdprotein)? 30\&.0 : 30\&.0)
.RE
.PP
\fB\-gapextend\fR \fIfloat\fR
.RS 4
Default value: @($(acdprotein)? 1\&.5 : 1\&.5)
.RE
.SS "Additional section"
.PP
\fB\-width\fR \fIinteger\fR
.RS 4
Default value: 16
.RE
.PP
\fB\-wordlen\fR \fIinteger\fR
.RS 4
Default value: 6
.RE
.PP
\fB\-limitmatch\fR \fIinteger\fR
.RS 4
.RE
.PP
\fB\-limitalign\fR \fIinteger\fR
.RS 4
.RE
.PP
\fB\-lowmatch\fR \fIinteger\fR
.RS 4
.RE
.PP
\fB\-lowalign\fR \fIinteger\fR
.RS 4
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIalign\fR
.RS 4
.RE
.PP
\fB\-errorfile\fR \fIoutfile\fR
.RS 4
Error file to be written to Default value: wordfinder\&.error
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
wordfinder is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
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