'\" t
.\"     Title: SEQSEARCH
.\"    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 "SEQSEARCH" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian"
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.SH "NAME"
seqsearch \- Generate PSI\-BLAST hits (DHF file) from a DAF file\&.
.SH "SYNOPSIS"
.HP \w'\fBseqsearch\fR\ 'u
\fBseqsearch\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-inseqspath\ \fR\fB\fIdirlist\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIinteger\fR\fR \fB\-evalue\ \fR\fB\fIfloat\fR\fR \fB\-maxhits\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBseqsearch\fR\ 'u
\fBseqsearch\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBseqsearch\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\-mode\fR \fIlist\fR
.RS 4
This option specifies the mode of SEQSEARCH operation\&. SEQSEARCH takes as input a directory of either i\&. single sequences, ii\&. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file))\&. The user has to specify which\&. Default value: 1
.RE
.PP
\fB\-inseqspath\fR \fIdirlist\fR
.RS 4
This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
.RE
.PP
\fB\-database\fR \fIstring\fR
.RS 4
Default value: swissprot
.RE
.SS "Required section"
.PP
\fB\-niter\fR \fIinteger\fR
.RS 4
This option specifies the number of PSIBLAST iterations\&. This option specifies the number of PSIBLAST iterations that are performed in a search\&. Default value: 1
.RE
.PP
\fB\-evalue\fR \fIfloat\fR
.RS 4
This option specifies the threshold E\-value for inclusion in family\&. This option specifies the threshold E\-value for a PSIBLAST hit to be retained\&. Default value: 0\&.001
.RE
.PP
\fB\-maxhits\fR \fIinteger\fR
.RS 4
This option specifies the maximum number of hits\&. This option specifies the maximum number of PSIBLAST hit that are retained\&. It should normally be set high so that nothing is discarded\&. Default value: 1000
.RE
.SS "Output section"
.PP
\fB\-dhfoutdir\fR \fIoutdir\fR
.RS 4
This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA format\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while SEQSEARCH ran\&. Default value: seqsearch\&.log
.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
seqsearch 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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