[med-svn] r3726 - trunk/packages/embassy-domainatrix/trunk/debian/manpages
Charles Plessy
plessy at alioth.debian.org
Mon Aug 3 10:37:18 UTC 2009
Author: plessy
Date: 2009-08-03 10:37:17 +0000 (Mon, 03 Aug 2009)
New Revision: 3726
Added:
trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e
Modified:
trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e
Log:
Refreshed and added manual pages.
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,71 +1,78 @@
+'\" t
.\" Title: CATHPARSE
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "CATHPARSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "CATHPARSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-cathparse - Generates DCF file from raw CATH files.
+cathparse \- Generates DCF file from raw CATH files\&.
.SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBcathparse\fR\ 'u
\fBcathparse\fR \fB\-listfile\ \fR\fB\fIinfile\fR\fR \fB\-domfile\ \fR\fB\fIinfile\fR\fR \fB\-namesfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP 10
+.HP \w'\fBcathparse\fR\ 'u
\fBcathparse\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBcathparse\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-listfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of raw CATH classification file (caths\.list\.vX\.X) (input)\. The raw CATH parsable files (classification and description files) available from ftp\.biochem\.ucl\.ac\.uk (/pub/cathdata/v2\.4)\. Default value: caths\.list\.v2\.4
+This option specifies the name of raw CATH classification file (caths\&.list\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: caths\&.list\&.v2\&.4
.RE
.PP
\fB\-domfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of raw CATH classification file (domlist\.vX\.X) (input)\. The raw CATH parsable files (classification and description files) available from ftp\.biochem\.ucl\.ac\.uk (/pub/cathdata/v2\.4)\. Default value: domlist\.v2\.4
+This option specifies the name of raw CATH classification file (domlist\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: domlist\&.v2\&.4
.RE
.PP
\fB\-namesfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of raw CATH classification file (CAT\.names\.all\.vX\.X) (input)\. The raw CATH parsable files (classification and description files) available from ftp\.biochem\.ucl\.ac\.uk (/pub/cathdata/v2\.4)\. Default value: CAT\.names\.all\.v2\.4
+This option specifies the name of raw CATH classification file (CAT\&.names\&.all\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: CAT\&.names\&.all\&.v2\&.4
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of CATH DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: Ecath\.dat
+This option specifies the name of CATH DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: Ecath\&.dat
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the CATHPARSE log file\. Default value: cathparse\.log
+This option specifies the name of the CATHPARSE log file\&. Default value: cathparse\&.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)\.
+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
cathparse is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,114 +1,121 @@
+'\" t
.\" Title: DOMAINNR
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "DOMAINNR" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "DOMAINNR" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-domainnr - Removes redundant domains from a DCF file.
+domainnr \- Removes redundant domains from a DCF file\&.
.SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBdomainnr\fR\ 'u
\fBdomainnr\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-retain\ \fR\fB\fItoggle\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-threshlow\ \fR\fB\fIfloat\fR\fR \fB\-threshup\ \fR\fB\fIfloat\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-redoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBdomainnr\fR\ 'u
\fBdomainnr\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBdomainnr\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies name of DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+This option specifies name of DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
.RS 4
-This option specifies the residue substitution matrix\. This is used for sequence comparison\. Default value: EBLOSUM62
+This option specifies the residue substitution matrix\&. This is used for sequence comparison\&. Default value: EBLOSUM62
.RE
.PP
\fB\-retain\fR \fItoggle\fR
.RS 4
-This option specifies whether to write redundant domains to a separate file\. If this option is selected, redundant domains are written to a separate output file\. Default value: N
+This option specifies whether to write redundant domains to a separate file\&. If this option is selected, redundant domains are written to a separate output file\&. Default value: N
.RE
.SS "Required section"
.PP
\fB\-node\fR \fIlist\fR
.RS 4
-This option specifies the node for redundancy removal\. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\. For example by selecting \'Class\' entries belonging to the same Class will be non\-redundant\. Default value: 1
+This option specifies the node for redundancy removal\&. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\&. For example by selecting \'Class\' entries belonging to the same Class will be non\-redundant\&. Default value: 1
.RE
.PP
\fB\-mode\fR \fIlist\fR
.RS 4
-This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity\. All permutations of pair\-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\. Default value: 1
+This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity\&. All permutations of pair\-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1
.RE
.PP
\fB\-threshold\fR \fIfloat\fR
.RS 4
-This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\. Default value: 95\.0
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0
.RE
.PP
\fB\-threshlow\fR \fIfloat\fR
.RS 4
-This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\. Default value: 30\.0
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0
.RE
.PP
\fB\-threshup\fR \fIfloat\fR
.RS 4
-This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\. Default value: 90\.0
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0
.RE
.SS "Additional section"
.PP
\fB\-gapopen\fR \fIfloat\fR
.RS 4
-This option specifies the gap insertion penalty\. This is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
.RE
.PP
\fB\-gapextend\fR \fIfloat\fR
.RS 4
-This option specifies the gap extension penalty\. This is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
.RE
.SS "Advanced section"
.SS "Output section"
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of non\-redundant DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: test\.scop
+This option specifies the name of non\-redundant DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
.RE
.PP
\fB\-redoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) for redundant sequences (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+This option specifies the name of DCF file (domain classification file) for redundant sequences (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.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 domainnr ran\. Default value: domainnr\.log
+This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainnr ran\&. Default value: domainnr\&.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)\.
+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
domainnr is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,67 +1,74 @@
+'\" t
.\" Title: DOMAINRESO
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "DOMAINRESO" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "DOMAINRESO" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-domainreso - Remove low resolution domains from a DCF file.
+domainreso \- Remove low resolution domains from a DCF file\&.
.SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBdomainreso\fR\ 'u
\fBdomainreso\fR \fB\-cpdbpath\ \fR\fB\fIdirlist\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR
-.HP 11
+.HP \w'\fBdomainreso\fR\ 'u
\fBdomainreso\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBdomainreso\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)\.
+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\-cpdbpath\fR \fIdirlist\fR
.RS 4
-This option specifies the location of domain CCF file (clean coordinate files) (input)\. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\. The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\. Default value: \./
+This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
.RE
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+This option specifies the name of DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.SS "Required section"
.PP
\fB\-threshold\fR \fIfloat\fR
.RS 4
-This option specifies the threshold for inclusion (Angstroms)\. Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file\. Default value: 2\.8
+This option specifies the threshold for inclusion (Angstroms)\&. Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file\&. Default value: 2\&.8
.RE
.SS "Output section"
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: test\.scop
+This option specifies the name of DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
.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)\.
+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
domainreso is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,37 +1,45 @@
+'\" t
.\" Title: DOMAINSEQS
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "DOMAINSEQS" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "DOMAINSEQS" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-domainseqs - Adds sequence records to a DCF file.
+domainseqs \- Adds sequence records to a DCF file\&.
.SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBdomainseqs\fR\ 'u
\fBdomainseqs\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dpdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-getswiss\ \fR\fB\fItoggle\fR\fR \fB\-pdbtospfile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP 11
+.HP \w'\fBdomainseqs\fR\ 'u
\fBdomainseqs\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBdomainseqs\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+This option specifies the name of DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-dpdbdir\fR \fIdirectory\fR
.RS 4
-This option specifies the location of domain CCF file (clean coordinate files) (input)\. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\. Default value: \./
+This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
.RE
.PP
\fB\-getswiss\fR \fItoggle\fR
@@ -41,53 +49,52 @@
.PP
\fB\-pdbtospfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of the pdbcodes to swissprot indexing file\. The swissprot:PDB equivalence file is generated by PDBTOSP
+This option specifies the name of the pdbcodes to swissprot indexing file\&. The swissprot:PDB equivalence file is generated by PDBTOSP
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
.RS 4
-This option specifies the residue substitution matrix, which is used for sequence comparison\. Default value: EBLOSUM62
+This option specifies the residue substitution matrix, which is used for sequence comparison\&. Default value: EBLOSUM62
.RE
.SS "Required section"
.SS "Additional section"
.PP
\fB\-gapopen\fR \fIfloat\fR
.RS 4
-This option specifies the gap insertion penalty\. This is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
.RE
.PP
\fB\-gapextend\fR \fIfloat\fR
.RS 4
-This option specifies the gap extension penalty\. This is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
.RE
.SS "Output section"
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: domainseqs\.out
+This option specifies the name of DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: domainseqs\&.out
.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 domainseqs ran\. Default value: domainseqs\.log
+This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainseqs ran\&. Default value: domainseqs\&.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)\.
+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
domainseqs is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,37 +1,45 @@
+'\" t
.\" Title: DOMAINSSE
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "DOMAINSSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "DOMAINSSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-domainsse - Add secondary structure records to a DCF file.
+domainsse \- Add secondary structure records to a DCF file\&.
.SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBdomainsse\fR\ 'u
\fBdomainsse\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dccfdir\ \fR\fB\fIdirectory\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP 10
+.HP \w'\fBdomainsse\fR\ 'u
\fBdomainsse\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBdomainsse\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of the DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+This option specifies the name of the DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-dccfdir\fR \fIdirectory\fR
.RS 4
-This option specifies the location of the domain CCF file (clean coordinate files) (input)\. A \'clean cordinate file\' contains protein coordinate and derived data for a single PDB file (\'protein clean coordinate file\') or a single domain from SCOP or CATH (\'domain clean coordinate file\'), in CCF format (EMBL\-like)\. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\. Default value: \./
+This option specifies the location of the domain CCF file (clean coordinate files) (input)\&. A \'clean cordinate file\' contains protein coordinate and derived data for a single PDB file (\'protein clean coordinate file\') or a single domain from SCOP or CATH (\'domain clean coordinate file\'), in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
.RE
.SS "Required section"
.SS "Advanced section"
@@ -39,30 +47,29 @@
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the DCF file (domain classification file) with secondary structure records (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+This option specifies the name of the DCF file (domain classification file) with secondary structure records (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the DOMAINSSE log file\. Default value: domainsse\.log
+This option specifies the name of the DOMAINSSE log file\&. Default value: domainsse\&.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)\.
+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
domainsse is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
Added: trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -0,0 +1,271 @@
+'\" t
+.\" Title: LIBSCAN
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
+.\"
+.TH "LIBSCAN" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.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\fIbool\fR\fR \fB\-henik\ \fR\fB\fIbool\fR\fR \fB\-hmm\ \fR\fB\fIbool\fR\fR \fB\-sam\ \fR\fB\fIbool\fR\fR \fB\-pssm\ \fR\fB\fIbool\fR\fR \fB\-sig\ \fR\fB\fIbool\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\fIint\fR\fR \fB\-thresh\ \fR\fB\fIfloat\fR\fR \fB\-maxhit\ \fR\fB\fIint\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 \fIbool\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-henik\fR \fIbool\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-hmm\fR \fIbool\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sam\fR \fIbool\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-pssm\fR \fIbool\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-sig\fR \fIbool\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 \fIint\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-thresh\fR \fIfloat\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-maxhit\fR \fIint\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 \'scop classification file\' 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 at 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
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,57 +1,64 @@
+'\" t
.\" Title: LIBSCANOUT
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "LIBSCANOUT" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "LIBSCANOUT" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-libscanout - Reads a DHF file and writes a file of top-scoring Classes, Folds and Superfamilies.
+libscanout \- Reads a DHF file and writes a file of top\-scoring Classes, Folds and Superfamilies\&.
.SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBlibscanout\fR\ 'u
\fBlibscanout\fR \fB\-dhfinfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 11
+.HP \w'\fBlibscanout\fR\ 'u
\fBlibscanout\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBlibscanout\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)\.
+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\-dhfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the location of the DHF file (domain hits file) (input)\. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\. 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\.
+This option specifies the location of the DHF file (domain hits file) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. 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\&.
.RE
.SS "Required section"
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
-This option specifies the location of the summary file (output)\. The summary file contains lists of domain Classes, Superfamilies and Families rank\-ordered on the basis of score (highest\-scoring first)\.
+This option specifies the location of the summary file (output)\&. The summary file contains lists of domain Classes, Superfamilies and Families rank\-ordered on the basis of score (highest\-scoring first)\&.
.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)\.
+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
libscanout is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,78 +1,85 @@
+'\" t
.\" Title: SCOPPARSE
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "SCOPPARSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "SCOPPARSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-scopparse - Generate DCF file from raw SCOP files.
+scopparse \- Generate DCF file from raw SCOP files\&.
.SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBscopparse\fR\ 'u
\fBscopparse\fR \fB\-classfile\ \fR\fB\fIinfile\fR\fR \fB\-desinfile\ \fR\fB\fIinfile\fR\fR \fB\-nosegments\ \fR\fB\fIboolean\fR\fR \fB\-nomultichain\ \fR\fB\fIboolean\fR\fR [\fB\-nominor\ \fR\fB\fIboolean\fR\fR] \fB\-dcffile\ \fR\fB\fIoutfile\fR\fR
-.HP 10
+.HP \w'\fBscopparse\fR\ 'u
\fBscopparse\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBscopparse\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-classfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of raw SCOP classification file dir\.cla\.scop\.txt_X\.XX (input)\. This is the raw SCOP classification file available at http://scop\.mrc\-lmb\.cam\.ac\.uk/scop/parse/dir\.cla\.scop\.txt_1\.57\.
+This option specifies the name of raw SCOP classification file dir\&.cla\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP classification file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.cla\&.scop\&.txt_1\&.57\&.
.RE
.PP
\fB\-desinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of raw SCOP description file dir\.des\.scop\.txt_X\.XX (input)\. This is the raw SCOP description file available at http://scop\.mrc\-lmb\.cam\.ac\.uk/scop/parse/dir\.des\.scop\.txt_1\.57\.
+This option specifies the name of raw SCOP description file dir\&.des\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP description file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.des\&.scop\&.txt_1\&.57\&.
.RE
.SS "Required section"
.PP
\fB\-nosegments\fR \fIboolean\fR
.RS 4
-This option specifies whether to omit domains comprising of more than one segment\. This is necessary if a continuous residue sequence is required\. Default value: N
+This option specifies whether to omit domains comprising of more than one segment\&. This is necessary if a continuous residue sequence is required\&. Default value: N
.RE
.PP
\fB\-nomultichain\fR \fIboolean\fR
.RS 4
-This option specifies whether to omit domains comprising segments from more than one chain\. This is necessary if a continuous residue sequence is required\. Default value: N
+This option specifies whether to omit domains comprising segments from more than one chain\&. This is necessary if a continuous residue sequence is required\&. Default value: N
.RE
.SS "Additional section"
.PP
\fB\-nominor\fR \fIboolean\fR
.RS 4
-This option specifies whether to omit domains from minor classes (defined as anything not in class \'All alpha proteins\', \'All beta proteins\', \'Alpha and beta proteins (a/b)\' or \'Alpha and beta proteins (a+b)\')\. This is necessary or appropriate for many analyses\. Default value: N
+This option specifies whether to omit domains from minor classes (defined as anything not in class \'All alpha proteins\', \'All beta proteins\', \'Alpha and beta proteins (a/b)\' or \'Alpha and beta proteins (a+b)\')\&. This is necessary or appropriate for many analyses\&. Default value: N
.RE
.SS "Output section"
.PP
\fB\-dcffile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of SCOP DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from the SCOP or CATH databases\. The file is generated by using DOMAINER and is in DCF format (EMBL\-like)\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: test\.scop
+This option specifies the name of SCOP DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from the SCOP or CATH databases\&. The file is generated by using DOMAINER and is in DCF format (EMBL\-like)\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
.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)\.
+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
scopparse is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e 2009-08-03 05:30:15 UTC (rev 3725)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e 2009-08-03 10:37:17 UTC (rev 3726)
@@ -1,103 +1,110 @@
+'\" t
.\" Title: SSEMATCH
-.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 09/25/2007
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 08/03/2009
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
+.\" Source: EMBOSS 0.1.0+20090715
+.\" Language: English
.\"
-.TH "SSEMATCH" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.TH "SSEMATCH" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
-ssematch - Search a DCF file for secondary structure matches.
+ssematch \- Search a DCF file for secondary structure matches\&.
.SH "SYNOPSIS"
-.HP 9
-\fBssematch\fR \fB\-ssinfile\ \fR\fB\fIinfile\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-maxhits\ \fR\fB\fIinteger\fR\fR [\fB\-gapopenr\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextendr\ \fR\fB\fIfloat\fR\fR] [\fB\-gapopene\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextende\ \fR\fB\fIfloat\fR\fR] \fB\-outssfile\ \fR\fB\fIoutfile\fR\fR \fB\-outsefile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBssematch\fR\ 'u
+\fBssematch\fR \fB\-ssinfile\ \fR\fB\fIinfile\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-maxhits\ \fR\fB\fIinteger\fR\fR [\fB\-rgapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-rgapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-egapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-egapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outssfile\ \fR\fB\fIoutfile\fR\fR \fB\-outsefile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBssematch\fR\ 'u
\fBssematch\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBssematch\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-ssinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of the file of secondary structure (input)\.
+This option specifies the name of the file of secondary structure (input)\&.
.RE
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of the DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+This option specifies the name of the DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
.RS 4
-This option specifies the secondary structure substitution matrix\. Default value: SSSUB
+This option specifies the secondary structure substitution matrix\&. Default value: SSSUB
.RE
.SS "Required section"
.PP
\fB\-maxhits\fR \fIinteger\fR
.RS 4
-This option specifies the number of top\-scoring matches to report\. Default value: 5
+This option specifies the number of top\-scoring matches to report\&. Default value: 5
.RE
.SS "Additional section"
.PP
-\fB\-gapopenr\fR \fIfloat\fR
+\fB\-rgapopen\fR \fIfloat\fR
.RS 4
-This options specifies the gap insertion penalty for reside\-based alignment\. The gap insertion penalty is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+This options specifies the gap insertion penalty for reside\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
.RE
.PP
-\fB\-gapextendr\fR \fIfloat\fR
+\fB\-rgapextend\fR \fIfloat\fR
.RS 4
-This options specifies the gap extension penalty for residue\-based alignment\. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+This options specifies the gap extension penalty for residue\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
.RE
.PP
-\fB\-gapopene\fR \fIfloat\fR
+\fB\-egapopen\fR \fIfloat\fR
.RS 4
-This options specifies the gap insertion penalty for element\-based alignment\. The gap insertion penalty is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+This options specifies the gap insertion penalty for element\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
.RE
.PP
-\fB\-gapextende\fR \fIfloat\fR
+\fB\-egapextend\fR \fIfloat\fR
.RS 4
-This options specifies the gap extension penalty for secondary structure element\-based alignment\. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+This options specifies the gap extension penalty for secondary structure element\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
.RE
.SS "Output section"
.PP
\fB\-outssfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the file containing top\-scoring domains for residue\-based alinnment (output)\.A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\.
+This option specifies the name of the file containing top\-scoring domains for residue\-based alignment (output)\&.A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
.RE
.PP
\fB\-outsefile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the file containing top\-scoring domains for secondary structure element\-based alinnment (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\.
+This option specifies the name of the file containing top\-scoring domains for secondary structure element\-based alignment (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the ssematch log file (output)\. Default value: ssematch\.log
+This option specifies the name of the ssematch log file (output)\&. Default value: ssematch\&.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)\.
+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
ssematch is fully documented via the
\fBtfm\fR(1)
-system\.
+system\&.
.SH "AUTHOR"
.PP
-\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
-.sp -1n
-.IP "" 4
-Wrote the script used to autogenerate this manual page\.
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 2007 Debian EMBOSS Packaging Team
.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\.
+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
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