'\" t
.\"     Title: LIBSCAN
.\"    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: DOMAINATRIX 0.1.0+20100721
.\"  Language: English
.\"
.TH "LIBSCAN" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian"
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.SH "NAME"
libscan \- Diagnostic searches for protein families\&.
.SH "SYNOPSIS"
.HP \w'\fBlibscan\fR\ 'u
\fBlibscan\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-grib\ \fR\fB\fIboolean\fR\fR \fB\-henik\ \fR\fB\fIboolean\fR\fR \fB\-hmm\ \fR\fB\fIboolean\fR\fR \fB\-sam\ \fR\fB\fIboolean\fR\fR \fB\-pssm\ \fR\fB\fIboolean\fR\fR \fB\-sig\ \fR\fB\fIboolean\fR\fR \fB\-hmmpath\ \fR\fB\fIstring\fR\fR \fB\-hmmextn\ \fR\fB\fIstring\fR\fR \fB\-hmmoutpath\ \fR\fB\fIstring\fR\fR \fB\-hmmoutextn\ \fR\fB\fIstring\fR\fR \fB\-sampath\ \fR\fB\fIstring\fR\fR \fB\-samextn\ \fR\fB\fIstring\fR\fR \fB\-samoutpath\ \fR\fB\fIstring\fR\fR \fB\-samoutextn\ \fR\fB\fIstring\fR\fR \fB\-pssmpath\ \fR\fB\fIstring\fR\fR \fB\-pssmextn\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIinteger\fR\fR \fB\-thresh\ \fR\fB\fIfloat\fR\fR \fB\-maxhit\ \fR\fB\fIinteger\fR\fR \fB\-pssmoutpath\ \fR\fB\fIstring\fR\fR \fB\-pssmoutextn\ \fR\fB\fIstring\fR\fR \fB\-gbvpath\ \fR\fB\fIstring\fR\fR \fB\-gbvextn\ \fR\fB\fIstring\fR\fR \fB\-gbvgapo\ \fR\fB\fIfloat\fR\fR \fB\-gbvgape\ \fR\fB\fIfloat\fR\fR \fB\-gbvoutpath\ \fR\fB\fIstring\fR\fR \fB\-gbvoutextn\ \fR\fB\fIstring\fR\fR \fB\-hnfpath\ \fR\fB\fIstring\fR\fR \fB\-hnfextn\ \fR\fB\fIstring\fR\fR \fB\-hnfgapo\ \fR\fB\fIfloat\fR\fR \fB\-hnfgape\ \fR\fB\fIfloat\fR\fR \fB\-hnfoutpath\ \fR\fB\fIstring\fR\fR \fB\-hnfoutextn\ \fR\fB\fIstring\fR\fR \fB\-sigpath\ \fR\fB\fIstring\fR\fR \fB\-sigextn\ \fR\fB\fIstring\fR\fR \fB\-nterm\ \fR\fB\fIlist\fR\fR \fB\-sub\ \fR\fB\fImatrixf\fR\fR \fB\-siggapo\ \fR\fB\fIfloat\fR\fR \fB\-siggape\ \fR\fB\fIfloat\fR\fR \fB\-sigoutpath\ \fR\fB\fIstring\fR\fR \fB\-sigoutextn\ \fR\fB\fIstring\fR\fR \fB\-db\ \fR\fB\fIseqset\fR\fR \fB\-scopf\ \fR\fB\fIinfile\fR\fR
.HP \w'\fBlibscan\fR\ 'u
\fBlibscan\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBlibscan\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"
.PP
\fB\-mode\fR \fIlist\fR
.RS 4
libscan runs in one of two modes either (i) database search mode or (ii) library screen mode\&. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model\&. In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top\-scoring families) for each one\&. Default value: 2
.RE
.PP
\fB\-grib\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-henik\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-hmm\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-sam\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-pssm\fR \fIboolean\fR
.RS 4
Default value: Y
.RE
.PP
\fB\-sig\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-hmmpath\fR \fIstring\fR
.RS 4
Default value: \&./lib/
.RE
.PP
\fB\-hmmextn\fR \fIstring\fR
.RS 4
Default value: \&.hmm
.RE
.PP
\fB\-hmmoutpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-hmmoutextn\fR \fIstring\fR
.RS 4
Default value: \&.hmmout
.RE
.PP
\fB\-sampath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-samextn\fR \fIstring\fR
.RS 4
Default value: \&.mod
.RE
.PP
\fB\-samoutpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-samoutextn\fR \fIstring\fR
.RS 4
Default value: \&.samout
.RE
.PP
\fB\-pssmpath\fR \fIstring\fR
.RS 4
Default value: /data/structure/lib/pssm/
.RE
.PP
\fB\-pssmextn\fR \fIstring\fR
.RS 4
Default value: \&.chk
.RE
.PP
\fB\-niter\fR \fIinteger\fR
.RS 4
Default value: 1
.RE
.PP
\fB\-thresh\fR \fIfloat\fR
.RS 4
Default value: 100
.RE
.PP
\fB\-maxhit\fR \fIinteger\fR
.RS 4
Default value: 1000
.RE
.PP
\fB\-pssmoutpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-pssmoutextn\fR \fIstring\fR
.RS 4
Default value: \&.pssmout
.RE
.PP
\fB\-gbvpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-gbvextn\fR \fIstring\fR
.RS 4
Default value: \&.grib
.RE
.PP
\fB\-gbvgapo\fR \fIfloat\fR
.RS 4
Default value: 10\&.0
.RE
.PP
\fB\-gbvgape\fR \fIfloat\fR
.RS 4
Default value: 0\&.5
.RE
.PP
\fB\-gbvoutpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-gbvoutextn\fR \fIstring\fR
.RS 4
Default value: \&.gribout
.RE
.PP
\fB\-hnfpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-hnfextn\fR \fIstring\fR
.RS 4
Default value: \&.henik
.RE
.PP
\fB\-hnfgapo\fR \fIfloat\fR
.RS 4
Default value: 10\&.0
.RE
.PP
\fB\-hnfgape\fR \fIfloat\fR
.RS 4
Default value: 0\&.5
.RE
.PP
\fB\-hnfoutpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-hnfoutextn\fR \fIstring\fR
.RS 4
Default value: \&.henikout
.RE
.PP
\fB\-sigpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-sigextn\fR \fIstring\fR
.RS 4
Default value: \&.sig
.RE
.PP
\fB\-nterm\fR \fIlist\fR
.RS 4
Default value: 1
.RE
.PP
\fB\-sub\fR \fImatrixf\fR
.RS 4
Default value: EBLOSUM62
.RE
.PP
\fB\-siggapo\fR \fIfloat\fR
.RS 4
Default value: 10\&.0
.RE
.PP
\fB\-siggape\fR \fIfloat\fR
.RS 4
Default value: 0\&.5
.RE
.PP
\fB\-sigoutpath\fR \fIstring\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-sigoutextn\fR \fIstring\fR
.RS 4
Default value: \&.sigout
.RE
.PP
\fB\-db\fR \fIseqset\fR
.RS 4
In database search mode libscan scans each discriminating element against a sequence set\&. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements) Default value: 49142\&.vdhf
.RE
.PP
\fB\-scopf\fR \fIinfile\fR
.RS 4
In either mode, a \*(Aqscop classification file\*(Aq is required as a source of family classification data\&. A scop classification file contains classification and other data for domains from the scop database\&. The file is in embl\-like format and is generated by scopparse\&. Domain sequence information can be added to the file by using scopseqs\&. Default value: /data/structure/dcf/scop_raw\&.dcf
.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
libscan 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\&.
.sp