[med-svn] r3671 - in trunk/packages: . embassy-domsearch embassy-domsearch/trunk embassy-domsearch/trunk/debian embassy-domsearch/trunk/debian/manpages
Charles Plessy
plessy at alioth.debian.org
Mon Jul 20 02:21:52 UTC 2009
Author: plessy
Date: 2009-07-20 02:21:51 +0000 (Mon, 20 Jul 2009)
New Revision: 3671
Added:
trunk/packages/embassy-domsearch/
trunk/packages/embassy-domsearch/tags/
trunk/packages/embassy-domsearch/trunk/
trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e
Removed:
trunk/packages/embassy-domsearch/trunk/debian/embassy-domainatrix.manpages
trunk/packages/embassy-domsearch/trunk/debian/manpages/cathparse.1
trunk/packages/embassy-domsearch/trunk/debian/manpages/domainnr.1
trunk/packages/embassy-domsearch/trunk/debian/manpages/domainreso.1
trunk/packages/embassy-domsearch/trunk/debian/manpages/domainseqs.1
trunk/packages/embassy-domsearch/trunk/debian/manpages/domainsse.1
trunk/packages/embassy-domsearch/trunk/debian/manpages/libscanout.1
trunk/packages/embassy-domsearch/trunk/debian/manpages/scopparse.1
trunk/packages/embassy-domsearch/trunk/debian/manpages/ssematch.1
Modified:
trunk/packages/embassy-domsearch/trunk/debian/changelog
trunk/packages/embassy-domsearch/trunk/debian/control
trunk/packages/embassy-domsearch/trunk/debian/copyright
trunk/packages/embassy-domsearch/trunk/debian/watch
Log:
New EMBASSY package.
Property changes on: trunk/packages/embassy-domsearch/trunk
___________________________________________________________________
Added: svn:mergeinfo
+
Modified: trunk/packages/embassy-domsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/changelog 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/changelog 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,18 +1,5 @@
-embassy-domainatrix (0.1.0+20080715-1) unstable; urgency=low
+embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low
- * New upstream release in which the version number was unchanged.
- * debian/control:
- - Updated my email address.
- - Build against EMBOSS 6.
- - Using debhelper 7.
- - Checked conformance with Policy 3.8.0 (no changes needed).
- - Corrected DM-Upload-Allowed.
- * debian/copyright updated to latest format.
+ * Initial release (Closes: #537204).
- -- Charles Plessy <plessy at debian.org> Thu, 26 Feb 2009 09:57:33 +0900
-
-embassy-domainatrix (0.1.0-1) unstable; urgency=low
-
- * Initial release
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 25 Sep 2007 13:52:47 +0900
+ -- Charles Plessy <plessy at debian.org> Mon, 20 Jul 2009 10:43:26 +0900
Modified: trunk/packages/embassy-domsearch/trunk/debian/control
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/control 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/control 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,28 +1,27 @@
-Source: embassy-domainatrix
+Source: embassy-domsearch
Section: science
Priority: optional
Build-Depends: cdbs, debhelper (>= 7), libajax6-dev, libnucleus6-dev, emboss-lib, libx11-dev, libgd2-xpm-dev
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domainatrix/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domainatrix/trunk/
-Standards-Version: 3.8.0
-Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domsearch/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domsearch/trunk/
+Standards-Version: 3.8.2
+Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH
-Package: embassy-domainatrix
+Package: embassy-domsearch
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Recommends: emboss
Suggests: embassy
-Description: Extra EMBOSS commands to handle domain classification file
- The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP
+Description: Extra EMBOSS commands to search for protein domains
+ The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP
for their protein domain research. They are included as an EMBASSY package as
a work in progress.
.
- Applications in the current domainatrix release are cathparse (generates DCF
- file from raw CATH files), domainnr (removes redundant domains from a DCF
- file), domainreso (removes low resolution domains from a DCF file), domainseqs
- (adds sequence records to a DCF file), domainsse (adds secondary structure
- records to a DCF file), scopparse (generates DCF file from raw SCOP files) and
- ssematch (searches a DCF file for secondary structure matches).
+ Applications in this DOMSEARCH release are seqfraggle (removes fragment
+ sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch
+ (generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove
+ ambiguous classified sequences from DHF files) and seqwords (Generates DHF
+ files from keyword search of UniProt).
Modified: trunk/packages/embassy-domsearch/trunk/debian/copyright
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/copyright 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/copyright 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,43 +1,25 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=322
-Upstream-Name: DOMAINATRIX
-Upstream-Maintainer: Alan Bleasby (ableasby at ebi.ac.uk)
- Matt Blades
- Mike Hurley
- Jon Ison (jison at ebi.ac.uk)
- Amanda O'Reilly
- Ranjeeva Ranasinghe
-Upstream-Source: ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.0.tar.gz
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-Files: *
-Copyright: © Alan Bleasby (ableasby at ebi.ac.uk)
- Matt Blades
- Mike Hurley
- Jon Ison (jison at ebi.ac.uk)
- Amanda O'Reilly
- Ranjeeva Ranasinghe
+Name : DOMSEARCH
+Contact : Jon Ison (jison at ebi.ac.uk)
+Source : ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.0.tar.gz
+
+Copyright: Jon Ison (jison at ebi.ac.uk), Matt Blades, Ranjeeva Ranasinghe.
+
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
-.
+
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
-.
+
You should have received a copy of the GNU General Public License
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-.
- On Debian systems, the complete text of the GNU General
- Public License can be found in `/usr/share/common-licenses/GPL'.
-.
- Please cite the authors and EMBOSS.
-.
- Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open
- Software Suite. Trends in Genetics, 15:276-278.
-Files: debian/*
-Copyright: © 2007,2009 Charles Plessy
-License: Same as DOMAINATRIX
+On Debian systems, the complete text of the GNU General Public License version 2 can be
+found in ‘/usr/share/common-licenses/GPL-2’.
Deleted: trunk/packages/embassy-domsearch/trunk/debian/embassy-domainatrix.manpages
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/embassy-domainatrix.manpages 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,9 +0,0 @@
-debian/manpages/cathparse.1
-debian/manpages/domainnr.1
-debian/manpages/domainreso.1
-debian/manpages/domainseqs.1
-debian/manpages/domainsse.1
-#debian/manpages/libscan.1
-debian/manpages/libscanout.1
-debian/manpages/scopparse.1
-debian/manpages/ssematch.1
Added: trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages (rev 0)
+++ trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages 2009-07-20 02:21:51 UTC (rev 3671)
@@ -0,0 +1,5 @@
+debian/manpages/seqfraggle.1e
+debian/manpages/seqnr.1e
+debian/manpages/seqsearch.1e
+debian/manpages/seqsort.1e
+debian/manpages/seqwords.1e
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/cathparse.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/cathparse.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,71 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "CATHPARSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-cathparse - Generates DCF file from raw CATH files.
-.SH "SYNOPSIS"
-.HP 10
-\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
-\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)\.
-.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
-.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
-.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
-.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
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-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)\.
-.SH "SEE ALSO"
-.PP
-cathparse is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/domainnr.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/domainnr.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,114 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "DOMAINNR" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-domainnr - Removes redundant domains from a DCF file.
-.SH "SYNOPSIS"
-.HP 9
-\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
-\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)\.
-.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\.
-.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
-.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
-.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
-.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
-.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
-.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
-.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
-.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
-.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
-.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
-.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\.
-.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
-.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
-domainnr is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/domainreso.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/domainreso.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,67 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "DOMAINRESO" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-domainreso - Remove low resolution domains from a DCF file.
-.SH "SYNOPSIS"
-.HP 11
-\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
-\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)\.
-.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: \./
-.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\.
-.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
-.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
-.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
-domainreso is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/domainseqs.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/domainseqs.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,93 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "DOMAINSEQS" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-domainseqs - Adds sequence records to a DCF file.
-.SH "SYNOPSIS"
-.HP 11
-\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
-\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)\.
-.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\.
-.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: \./
-.RE
-.PP
-\fB\-getswiss\fR \fItoggle\fR
-.RS 4
-Default value: N
-.RE
-.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
-.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
-.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
-.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
-.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
-.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
-.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
-domainseqs is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/domainsse.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/domainsse.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,68 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "DOMAINSSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-domainsse - Add secondary structure records to a DCF file.
-.SH "SYNOPSIS"
-.HP 10
-\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
-\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)\.
-.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\.
-.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: \./
-.RE
-.SS "Required section"
-.SS "Advanced section"
-.SS "Output section"
-.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\.
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-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)\.
-.SH "SEE ALSO"
-.PP
-domainsse is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/libscanout.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/libscanout.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,57 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "LIBSCANOUT" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-libscanout - Reads a DHF file and writes a file of top-scoring Classes, Folds and Superfamilies.
-.SH "SYNOPSIS"
-.HP 11
-\fBlibscanout\fR \fB\-dhfinfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 11
-\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)\.
-.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\.
-.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)\.
-.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
-libscanout is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/scopparse.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/scopparse.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,78 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "SCOPPARSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-scopparse - Generate DCF file from raw SCOP files.
-.SH "SYNOPSIS"
-.HP 10
-\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
-\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)\.
-.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\.
-.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\.
-.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
-.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
-.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
-.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
-.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
-scopparse is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Added: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e (rev 0)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e 2009-07-20 02:21:51 UTC (rev 3671)
@@ -0,0 +1,69 @@
+'\" t
+.\" Title: SEQFRAGGLE
+.\" 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: 07/16/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0+20980715
+.\" Language: English
+.\"
+.TH "SEQFRAGGLE" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "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"
+seqfraggle \- Removes fragment sequences from DHF files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqfraggle\fR\ 'u
+\fBseqfraggle\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-thresh\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBseqfraggle\fR\ 'u
+\fBseqfraggle\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqfraggle\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\-dhfinpath\fR \fIdirlist\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) or other sequence files (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\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./
+.RE
+.SS "Required section"
+.PP
+\fB\-thresh\fR \fIinteger\fR
+.RS 4
+This option specifies the percentage of median length for definition of fragments\&. SEQFRAGGLE first determines the median length of all the sequences in the input file, then discards any hit sequences which are not within a threshold percentage of the median length\&. The remaining sequences are written to the output file\&. Default value: 50
+.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 \'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\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./
+.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
+seqfraggle 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
Added: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e (rev 0)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e 2009-07-20 02:21:51 UTC (rev 3671)
@@ -0,0 +1,135 @@
+'\" t
+.\" Title: SEQNR
+.\" 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: 07/16/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0+20980715
+.\" Language: English
+.\"
+.TH "SEQNR" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "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"
+seqnr \- Removes redundancy from DHF files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqnr\fR\ 'u
+\fBseqnr\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dosing\ \fR\fB\fItoggle\fR\fR \fB\-singletsdir\ \fR\fB\fIdirectory\fR\fR \fB\-dosets\ \fR\fB\fItoggle\fR\fR \fB\-insetsdir\ \fR\fB\fIdirectory\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-thresh\ \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\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-dored\ \fR\fB\fItoggle\fR\fR \fB\-redoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqnr\fR\ 'u
+\fBseqnr\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqnr\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)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dhfinpath\fR \fIdirlist\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\-dosing\fR \fItoggle\fR
+.RS 4
+This option specifies whether to use singlet sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y
+.RE
+.PP
+\fB\-singletsdir\fR \fIdirectory\fR
+.RS 4
+This option specifies the location of singlet filter sequences (e\&.g\&. DHF files) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\-dosets\fR \fItoggle\fR
+.RS 4
+This option specifies whether to use sets of sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y
+.RE
+.PP
+\fB\-insetsdir\fR \fIdirectory\fR
+.RS 4
+This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. A \'domain alignment file\' 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\-matrix\fR \fImatrixf\fR
+.RS 4
+This option specifies the residue substitution matrix that is used for sequence comparison\&. Default value: EBLOSUM62
+.RE
+.SS "Required section"
+.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 set of input sequences 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\-thresh\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold\&. The % sequence identity redundancy threshold 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 (lower limit)\&. The % sequence identity redundancy threshold 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 (upper limit)\&. The % sequence identity redundancy threshold 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\&. 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\-gapextend\fR \fIfloat\fR
+.RS 4
+This option specifies the gap extension penalty\&. 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\-dhfoutdir\fR \fIoutdir\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\-dored\fR \fItoggle\fR
+.RS 4
+This option specifies whether to retain redundant sequences\&. If this option is set a DHF file (domain hits file) of redundant sequences is written\&. Default value: N
+.RE
+.PP
+\fB\-redoutdir\fR \fIoutdir\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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 SEQNR log file (output)\&. The log file contains messages about any errors arising while SEQNR ran\&. Default value: seqnr\&.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
+seqnr 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
Added: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e (rev 0)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e 2009-07-20 02:21:51 UTC (rev 3671)
@@ -0,0 +1,94 @@
+'\" t
+.\" Title: SEQSEARCH
+.\" 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: 07/16/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0+20980715
+.\" Language: English
+.\"
+.TH "SEQSEARCH" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "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"
+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 \'domain alignment file\' 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 \'domain hits file\' 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 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
Added: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e (rev 0)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e 2009-07-20 02:21:51 UTC (rev 3671)
@@ -0,0 +1,89 @@
+'\" t
+.\" Title: SEQSORT
+.\" 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: 07/16/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0+20980715
+.\" Language: English
+.\"
+.TH "SEQSORT" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "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"
+seqsort \- Remove ambiguous classified sequences from DHF files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqsort\fR\ 'u
+\fBseqsort\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-dofamilies\ \fR\fB\fItoggle\fR\fR \fB\-doambiguities\ \fR\fB\fItoggle\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-hitsfile\ \fR\fB\fIoutfile\fR\fR \fB\-ambigfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqsort\fR\ 'u
+\fBseqsort\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqsort\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\-dhfindir\fR \fIdirectory\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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
+.SS "Required section"
+.PP
+\fB\-overlap\fR \fIinteger\fR
+.RS 4
+This option specifies the number of overlapping residues required for merging of two hits\&. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user\-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits\&. Default value: 10
+.RE
+.PP
+\fB\-dofamilies\fR \fItoggle\fR
+.RS 4
+This option specifies to write a domain families file\&. If this option is set a domain families file is written\&. Default value: N
+.RE
+.PP
+\fB\-doambiguities\fR \fItoggle\fR
+.RS 4
+This option specifies whether to write a domain ambiguities file\&. If this option is set a domain ambiguities file is written\&. Default value: N
+.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 \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\-hitsfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of domain families file (output)\&. A \'domain families file\' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \'domain ambiguities file\'\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf
+.RE
+.PP
+\fB\-ambigfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of domain ambiguities file (output)\&. A \'domain families file\' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \'domain ambiguities file\'\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf
+.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
+seqsort 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
Added: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e (rev 0)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e 2009-07-20 02:21:51 UTC (rev 3671)
@@ -0,0 +1,68 @@
+'\" t
+.\" Title: SEQWORDS
+.\" 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: 07/16/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0+20980715
+.\" Language: English
+.\"
+.TH "SEQWORDS" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "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"
+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 \'domain hits file\' 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 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
Deleted: trunk/packages/embassy-domsearch/trunk/debian/manpages/ssematch.1
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/ssematch.1 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,103 +0,0 @@
-.\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0
-.\"
-.TH "SSEMATCH" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-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
-\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)\.
-.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)\.
-.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\.
-.RE
-.PP
-\fB\-datafile\fR \fImatrixf\fR
-.RS 4
-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
-.RE
-.SS "Additional section"
-.PP
-\fB\-gapopenr\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
-.RE
-.PP
-\fB\-gapextendr\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
-.RE
-.PP
-\fB\-gapopene\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
-.RE
-.PP
-\fB\-gapextende\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
-.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)\.
-.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)\.
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-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)\.
-.SH "SEE ALSO"
-.PP
-ssematch is fully documented via the
-\fBtfm\fR(1)
-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\.
-.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\.
-.sp
Modified: trunk/packages/embassy-domsearch/trunk/debian/watch
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/watch 2009-07-15 15:12:39 UTC (rev 3642)
+++ trunk/packages/embassy-domsearch/trunk/debian/watch 2009-07-20 02:21:51 UTC (rev 3671)
@@ -1,2 +1,3 @@
version=3
-ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-(.*)\.tar\.gz debian uupdate
+opts=dversionmangle=s/\+\d+// \
+ ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-(.*).tar.gz
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