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.\"     Title: SEQWORDS
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\"      Date: 08/11/2010
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: DOMSEARCH 0.1.0++20100721
.\"  Language: English
.\"
.TH "SEQWORDS" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian"
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.SH "NAME"
seqwords \- Generates DHF files from keyword search of UniProt\&.
.SH "SYNOPSIS"
.HP \w'\fBseqwords\fR\ 'u
\fBseqwords\fR \fB\-keyfile\ \fR\fB\fIinfile\fR\fR \fB\-spfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBseqwords\fR\ 'u
\fBseqwords\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBseqwords\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-keyfile\fR \fIinfile\fR
.RS 4
This option specifies the name of keywords file (input)\&. This contains a list of keywords specific to a number of SCOP or CATH families and superfamilies used by SEQWORDS to search a sequence database\&.
.RE
.PP
\fB\-spfile\fR \fIinfile\fR
.RS 4
This option specifies the name of the sequence database (input) to search\&.
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of the DHF file (domain hits file) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits
.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
seqwords 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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