--- embassy-domsearch-0.1.0+20980715.orig/debian/embassy-domsearch.manpages +++ embassy-domsearch-0.1.0+20980715/debian/embassy-domsearch.manpages @@ -0,0 +1,5 @@ +debian/manpages/seqfraggle.1e +debian/manpages/seqnr.1e +debian/manpages/seqsearch.1e +debian/manpages/seqsort.1e +debian/manpages/seqwords.1e --- embassy-domsearch-0.1.0+20980715.orig/debian/control +++ embassy-domsearch-0.1.0+20980715/debian/control @@ -0,0 +1,27 @@ +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 +DM-Upload-Allowed: yes +Uploaders: Charles Plessy +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-domsearch +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: emboss +Suggests: embassy +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 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). --- embassy-domsearch-0.1.0+20980715.orig/debian/changelog +++ embassy-domsearch-0.1.0+20980715/debian/changelog @@ -0,0 +1,5 @@ +embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low + + * Initial release (Closes: #537204). + + -- Charles Plessy Mon, 20 Jul 2009 10:43:26 +0900 --- embassy-domsearch-0.1.0+20980715.orig/debian/rules +++ embassy-domsearch-0.1.0+20980715/debian/rules @@ -0,0 +1,6 @@ +#!/usr/bin/make -f + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/autotools.mk + +CFLAGS += -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/nucleus --- embassy-domsearch-0.1.0+20980715.orig/debian/copyright +++ embassy-domsearch-0.1.0+20980715/debian/copyright @@ -0,0 +1,25 @@ +Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’. + +Name : DOMSEARCH +Contact : Jon Ison (jison@ebi.ac.uk) +Source : ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.0.tar.gz + +Copyright: Jon Ison (jison@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 version 2 can be +found in ‘/usr/share/common-licenses/GPL-2’. --- embassy-domsearch-0.1.0+20980715.orig/debian/watch +++ embassy-domsearch-0.1.0+20980715/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts=dversionmangle=s/\+\d+// \ + ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-(.*).tar.gz --- embassy-domsearch-0.1.0+20980715.orig/debian/manpages/seqsearch.1e +++ embassy-domsearch-0.1.0+20980715/debian/manpages/seqsearch.1e @@ -0,0 +1,94 @@ +'\" t +.\" Title: SEQSEARCH +.\" Author: Debian-Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.1 +.\" 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@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 --- embassy-domsearch-0.1.0+20980715.orig/debian/manpages/seqnr.1e +++ embassy-domsearch-0.1.0+20980715/debian/manpages/seqnr.1e @@ -0,0 +1,135 @@ +'\" t +.\" Title: SEQNR +.\" Author: Debian-Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.1 +.\" 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@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 --- embassy-domsearch-0.1.0+20980715.orig/debian/manpages/seqsort.1e +++ embassy-domsearch-0.1.0+20980715/debian/manpages/seqsort.1e @@ -0,0 +1,89 @@ +'\" t +.\" Title: SEQSORT +.\" Author: Debian-Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.1 +.\" 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@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 --- embassy-domsearch-0.1.0+20980715.orig/debian/manpages/seqfraggle.1e +++ embassy-domsearch-0.1.0+20980715/debian/manpages/seqfraggle.1e @@ -0,0 +1,69 @@ +'\" t +.\" Title: SEQFRAGGLE +.\" Author: Debian-Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.1 +.\" 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@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 --- embassy-domsearch-0.1.0+20980715.orig/debian/manpages/seqwords.1e +++ embassy-domsearch-0.1.0+20980715/debian/manpages/seqwords.1e @@ -0,0 +1,68 @@ +'\" t +.\" Title: SEQWORDS +.\" Author: Debian-Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.1 +.\" 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@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