[med-svn] r1190 - trunk/packages/glam2/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Wed Jan 23 01:08:39 UTC 2008
Author: charles-guest
Date: 2008-01-23 01:08:39 +0000 (Wed, 23 Jan 2008)
New Revision: 1190
Added:
trunk/packages/glam2/trunk/debian/glam2.1.xml
trunk/packages/glam2/trunk/debian/glam2format.1
trunk/packages/glam2/trunk/debian/glam2format.1.xml
trunk/packages/glam2/trunk/debian/glam2scan.1
trunk/packages/glam2/trunk/debian/glam2scan.1.xml
Modified:
trunk/packages/glam2/trunk/debian/glam2.1
Log:
writing manpages
Modified: trunk/packages/glam2/trunk/debian/glam2.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.1 2008-01-22 16:49:46 UTC (rev 1189)
+++ trunk/packages/glam2/trunk/debian/glam2.1 2008-01-23 01:08:39 UTC (rev 1190)
@@ -1,65 +1,174 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH GLAM2 1 "November 13, 2007"
-.\" Please adjust this date whenever revising the manpage.
+.\" Title: GLAM2
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 01/23/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-glam2 \- detects gapped motifs in unaligned biological sequences
-.SH SYNOPSIS
-.B glam2
-.RI [ options ] " files" ...
-.br
-.B glam2format
-.RI [ options ] " files" ...
-.br
-.B glam2mask
-.RI [ options ] " files" ...
-.br
-.B glam2scan
-.RI [ options ] " files" ...
-.SH DESCRIPTION
-This manual page documents briefly the
-.B glam2
-and
-.B bar
-commands.
+.TH "GLAM2" "1" "01/23/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2 - Gapped Local Alignment of Motifs
+.SH "SYNOPSIS"
+.HP 6
+\fBglam2\fR [\fBoptions\fR] \fBalphabet\fR \fImy_seqs\.fa\fR
.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBglam2\fP is a program that...
-.SH OPTIONS
-These programs follow the usual GNU command line syntax, with long
-options starting with two dashes (`-').
-A summary of options is included below.
-For a complete description, see the Info files.
-.TP
-.B \-h, \-\-help
-Show summary of options.
-.TP
-.B \-v, \-\-version
-Show version of program.
-.SH SEE ALSO
-.BR bar (1),
-.BR baz (1).
-.br
-The programs are documented fully by
-.IR "The Rise and Fall of a Fooish Bar" ,
-available via the Info system.
-.SH AUTHOR
-glam2 was written by <upstream author>.
+An alphabet other than
+\fIp\fR
+or
+\fIn\fR
+is interpreted as the name of an alphabet file\.
+.SH "DESCRIPTION"
.PP
-This manual page was written by Steffen Moeller <moeller at debian.org>,
-for the Debian project (but may be used by others).
+GLAM2 is a software package for finding motifs in sequences, typically amino\-acid or nucleotide sequences\. A motif is a re\-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif\. The main innovation of GLAM2 is that it allows insertions and deletions in motifs\.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-h\fR
+.RS 4
+Show all options and their default settings\.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\.
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+Number of alignment runs (\fI10\fR)\.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+End each run after this many iterations without improvement (\fI10000\fR)\.
+.RE
+.PP
+\fB\-2\fR
+.RS 4
+Examine both strands \- forward and reverse complement\.
+.RE
+.PP
+\fB\-z\fR
+.RS 4
+Minimum number of sequences in the alignment (\fI2\fR)\.
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+Minimum number of aligned columns (\fI2\fR)\.
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+Maximum number of aligned columns (\fI50\fR)\.
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+Initial number of aligned columns (\fI20\fR)\.
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+Dirichlet mixture file\.
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Deletion pseudocount (\fI0\.1\fR)\.
+.RE
+.PP
+\fB\-E\fR
+.RS 4
+No\-deletion pseudocount (\fI2\.0\fR)\.
+.RE
+.PP
+\fB\-I\fR
+.RS 4
+Insertion pseudocount (\fI0\.02\fR)\.
+.RE
+.PP
+\fB\-J\fR
+.RS 4
+No\-insertion pseudocount (\fI1\.0\fR)\.
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Weight for generic versus sequence\-set\-specific residue abundances (\fI1e+99\fR)\.
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+Initial temperature (\fI1\.2\fR)\.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Cooling factor per n iterations (\fI1\.44\fR)\.
+.RE
+.PP
+\fB\-u\fR
+.RS 4
+Temperature lower bound (\fI0\.1\fR)\.
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+Print progress information at each iteration\.
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Column\-sampling moves per site\-sampling move (\fI1\.0\fR)\.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Site sampling algorithm:
+\fI0\fR=FAST
+\fI1\fR=SLOW
+\fI2\fR=FFT (\fI0\fR)\.
+.RE
+.PP
+\fB\-s\fR
+.RS 4
+Seed for pseudo\-random numbers (\fI1\fR)\.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\.org\.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain
+.sp
Added: trunk/packages/glam2/trunk/debian/glam2.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.1.xml (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2.1.xml 2008-01-23 01:08:39 UTC (rev 1190)
@@ -0,0 +1,272 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1056">
+ <!ENTITY dhtitle "glam2 Manual">
+ <!ENTITY dhucpackage "GLAM2">
+ <!ENTITY dhpackage "glam2">
+ <!ENTITY dhproduct "GLAM2">
+ <!ENTITY dhsection "1">
+
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <!-- Better put a suite name instead of &dhpackage; into productname -->
+ <productname>&dhproduct;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Martin</firstname>
+ <firstname>C</firstname>
+ <surname>Frith</surname>
+ <contrib>Author of GLAM2</contrib>
+ </author>
+ <author>
+ <firstname>Timothy</firstname>
+ <firstname>L</firstname>
+ <surname>Bailey</surname>
+ <contrib>Author of GLAM2</contrib>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Formatted this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <legalnotice>
+ <para>The source code and the documentation of GLAM2 are released in the public domain</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Gapped Local Alignment of Motifs</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>options</option></arg>
+ <arg choice="plain"><option>alphabet</option></arg>
+ <arg choice="plain"><replaceable>my_seqs.fa</replaceable></arg>
+ </cmdsynopsis>
+ <para>An alphabet other than <parameter>p</parameter> or <parameter>n</parameter> is interpreted as the name of an alphabet file.</para>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.
+ </para>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS (default settings)</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>-h</option></term>
+ <listitem>
+ <para>Show all options and their default settings.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-o</option></term>
+ <listitem>
+ <para>Output file (<parameter>stdout</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-r</option></term>
+ <listitem>
+ <para>Number of alignment runs (<parameter>10</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-n</option></term>
+ <listitem>
+ <para>End each run after this many iterations without improvement (<parameter>10000</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-2</option></term>
+ <listitem>
+ <para>Examine both strands - forward and reverse complement.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-z</option></term>
+ <listitem>
+ <para>Minimum number of sequences in the alignment (<parameter>2</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-a</option></term>
+ <listitem>
+ <para>Minimum number of aligned columns (<parameter>2</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-b</option></term>
+ <listitem>
+ <para>Maximum number of aligned columns (<parameter>50</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-w</option></term>
+ <listitem>
+ <para>Initial number of aligned columns (<parameter>20</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-d</option></term>
+ <listitem>
+ <para>Dirichlet mixture file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-D</option></term>
+ <listitem>
+ <para>Deletion pseudocount (<parameter>0.1</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-E</option></term>
+ <listitem>
+ <para>No-deletion pseudocount (<parameter>2.0</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-I</option></term>
+ <listitem>
+ <para>Insertion pseudocount (<parameter>0.02</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-J</option></term>
+ <listitem>
+ <para>No-insertion pseudocount (<parameter>1.0</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-q</option></term>
+ <listitem>
+ <para>Weight for generic versus sequence-set-specific residue abundances (<parameter>1e+99</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-t</option></term>
+ <listitem>
+ <para>Initial temperature (<parameter>1.2</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-c</option></term>
+ <listitem>
+ <para>Cooling factor per n iterations (<parameter>1.44</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-u</option></term>
+ <listitem>
+ <para>Temperature lower bound (<parameter>0.1</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-p</option></term>
+ <listitem>
+ <para>Print progress information at each iteration.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-m</option></term>
+ <listitem>
+ <para>Column-sampling moves per site-sampling move (<parameter>1.0</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-x</option></term>
+ <listitem>
+ <para>Site sampling algorithm: <parameter>0</parameter>=FAST <parameter>1</parameter>=SLOW <parameter>2</parameter>=FFT (<parameter>0</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-s</option></term>
+ <listitem>
+ <para>Seed for pseudo-random numbers (<parameter>1</parameter>).</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>glam2format</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2mask</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2-purge</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2scan</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry></para>
+ <para>The full Hypertext documentation of GLAM2 is available online at <ulink url="http://bioinformatics.org.au/glam2/">http://bioinformatics.org.au/glam2/</ulink> or on this computer in <filename class="directory">/usr/share/doc/glam2/</filename>.</para>
+ </refsect1>
+
+ <refsect1 id="ref">
+ <title>REFERENCE</title>
+ <para>
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+ </para>
+ </refsect1>
+</refentry>
Added: trunk/packages/glam2/trunk/debian/glam2format.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2format.1 (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2format.1 2008-01-23 01:08:39 UTC (rev 1190)
@@ -0,0 +1,86 @@
+.\" Title: GLAM2FORMAT
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 01/23/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2FORMAT" "1" "01/23/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2format - Gapped Local Alignment of Motifs
+.SH "SYNOPSIS"
+.HP 12
+\fBglam2format\fR [\fBoptions\fR] \fBmy_format\fR \fImy_motif\.glam2\fR
+.PP
+Formats: fasta, msf\.
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2format\fR
+reads in a motif found by
+\fBglam2\fR, and writes it in a standard alignment format (FASTA\-with\-gaps or MSF)\. This enables the alignment to be passed to third\-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo\. On the other hand, not all the motif information is preserved: in particular, the key positions are lost\. Only the top motif in
+\fBglam2\fR
+output is converted\.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Make a compact alignment\. By default, residues that are inserted between key positions are written as unaligned with each other\. This best reflects
+\fBglam2\fR\'s intention, but it can make the alignment large and full of gaps\. With
+\fI\-c\fR, inserted residues are written as arbitrarily aligned with each other, just as they appear in the
+\fBglam2\fR
+output\.
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Sequence file to make a
+\(lqglobal\(rq
+alignment by adding flanking sequences from the original FASTA\-format sequence file\. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the
+\fI\-c\fR
+option\. The sequences should have unique names and their order should be unchanged\.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBboxshade\fR(1),
+\fBglam2\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\.org\.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain
+.sp
Added: trunk/packages/glam2/trunk/debian/glam2format.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2format.1.xml (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2format.1.xml 2008-01-23 01:08:39 UTC (rev 1190)
@@ -0,0 +1,140 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1056">
+ <!ENTITY dhtitle "glam2 Manual">
+ <!ENTITY dhucpackage "GLAM2FORMAT">
+ <!ENTITY dhpackage "glam2format">
+ <!ENTITY dhproduct "GLAM2">
+ <!ENTITY dhsection "1">
+
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhproduct;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Martin</firstname>
+ <firstname>C</firstname>
+ <surname>Frith</surname>
+ <contrib>Author of GLAM2</contrib>
+ </author>
+ <author>
+ <firstname>Timothy</firstname>
+ <firstname>L</firstname>
+ <surname>Bailey</surname>
+ <contrib>Author of GLAM2</contrib>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Formatted this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <legalnotice>
+ <para>The source code and the documentation of GLAM2 are released in the public domain</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Gapped Local Alignment of Motifs</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>options</option></arg>
+ <arg choice="plain"><option>my_format</option></arg>
+ <arg choice="plain"><replaceable>my_motif.glam2</replaceable></arg>
+ </cmdsynopsis>
+ <para>Formats: fasta, msf.</para>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ <command>&dhpackage;</command> reads in a motif found by <command>glam2</command>, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in <command>glam2</command> output is converted.
+ </para>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS (default settings)</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+
+ <varlistentry>
+ <term><option>-o</option></term>
+ <listitem>
+ <para>Output file (<parameter>stdout</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-c</option></term>
+ <listitem>
+ <para>Make a compact alignment. By default, residues that are inserted between key positions are written as unaligned with each other. This best reflects <command>glam2</command>'s intention, but it can make the alignment large and full of gaps. With <varname>-c</varname>, inserted residues are written as arbitrarily aligned with each other, just as they appear in the <command>glam2</command> output.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-f</option></term>
+ <listitem>
+ <para>Sequence file to make a <quote>global</quote> alignment by adding flanking sequences from the original FASTA-format sequence file. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the <varname>-c</varname> option. The sequences should have unique names and their order should be unchanged.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry><refentrytitle>boxshade</refentrytitle>
+ <manvolnum>1</manvolnum></citerefentry>, <citerefentry>
+ <refentrytitle>glam2</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2mask</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2-purge</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2scan</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry></para>
+ <para>The full Hypertext documentation of GLAM2 is available online at <ulink url="http://bioinformatics.org.au/glam2/">http://bioinformatics.org.au/glam2/</ulink> or on this computer in <filename class="directory">/usr/share/doc/glam2/</filename>.</para>
+ </refsect1>
+
+ <refsect1 id="ref">
+ <title>REFERENCE</title>
+ <para>
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+ </para>
+ </refsect1>
+</refentry>
Added: trunk/packages/glam2/trunk/debian/glam2scan.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2scan.1 (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2scan.1 2008-01-23 01:08:39 UTC (rev 1190)
@@ -0,0 +1,109 @@
+.\" Title: GLAM2SCAN
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 01/23/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2SCAN" "1" "01/23/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2scan - Gapped Local Alignment of Motifs
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2scan\fR [\fBoptions\fR] \fBalphabet\fR \fImy_motif\.glam2\fR \fImy_seqs\.fa\fR
+.PP
+An alphabet other than
+\fIp\fR
+or
+\fIn\fR
+is interpreted as the name of an alphabet file\.
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2scan\fR
+finds matches, in a sequence database, to a motif discovered by
+\fBglam2\fR\. Each match receives a score, indicating how well it fits the motif\.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-h\fR
+.RS 4
+Show all options and their default settings\.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+Number of alignments to report (\fI25\fR)\.
+.RE
+.PP
+\fB\-2\fR
+.RS 4
+Examine both strands \- forward and reverse complement\.
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Deletion pseudocount (\fI0\.1\fR)\.
+.RE
+.PP
+\fB\-E\fR
+.RS 4
+No\-deletion pseudocount (\fI2\.0\fR)\.
+.RE
+.PP
+\fB\-I\fR
+.RS 4
+Insertion pseudocount (\fI0\.02\fR)\.
+.RE
+.PP
+\fB\-J\fR
+.RS 4
+No\-insertion pseudocount (\fI1\.0\fR)\.
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+Dirichlet mixture file\.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\.org\.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain
+.sp
Added: trunk/packages/glam2/trunk/debian/glam2scan.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2scan.1.xml (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2scan.1.xml 2008-01-23 01:08:39 UTC (rev 1190)
@@ -0,0 +1,182 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1056">
+ <!ENTITY dhtitle "glam2 Manual">
+ <!ENTITY dhucpackage "GLAM2SCAN">
+ <!ENTITY dhpackage "glam2scan">
+ <!ENTITY dhproduct "GLAM2">
+ <!ENTITY dhsection "1">
+
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <!-- Better put a suite name instead of &dhpackage; into productname -->
+ <productname>&dhproduct;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Martin</firstname>
+ <firstname>C</firstname>
+ <surname>Frith</surname>
+ <contrib>Author of GLAM2</contrib>
+ </author>
+ <author>
+ <firstname>Timothy</firstname>
+ <firstname>L</firstname>
+ <surname>Bailey</surname>
+ <contrib>Author of GLAM2</contrib>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Formatted this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <legalnotice>
+ <para>The source code and the documentation of GLAM2 are released in the public domain</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Gapped Local Alignment of Motifs</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>options</option></arg>
+ <arg choice="plain"><option>alphabet</option></arg>
+ <arg choice="plain"><replaceable>my_motif.glam2</replaceable></arg>
+ <arg choice="plain"><replaceable>my_seqs.fa</replaceable></arg>
+ </cmdsynopsis>
+ <para>An alphabet other than <parameter>p</parameter> or <parameter>n</parameter> is interpreted as the name of an alphabet file.</para>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ <command>glam2scan</command> finds matches, in a sequence database, to a motif discovered by <command>glam2</command>. Each match receives a score, indicating how well it fits the motif.
+ </para>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS (default settings)</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>-h</option></term>
+ <listitem>
+ <para>Show all options and their default settings.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-o</option></term>
+ <listitem>
+ <para>Output file (<parameter>stdout</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-n</option></term>
+ <listitem>
+ <para>Number of alignments to report (<parameter>25</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-2</option></term>
+ <listitem>
+ <para>Examine both strands - forward and reverse complement.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-D</option></term>
+ <listitem>
+ <para>Deletion pseudocount (<parameter>0.1</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-E</option></term>
+ <listitem>
+ <para>No-deletion pseudocount (<parameter>2.0</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-I</option></term>
+ <listitem>
+ <para>Insertion pseudocount (<parameter>0.02</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-J</option></term>
+ <listitem>
+ <para>No-insertion pseudocount (<parameter>1.0</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-d</option></term>
+ <listitem>
+ <para>Dirichlet mixture file.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>glam2format</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2mask</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2-purge</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry></para>
+ <para>The full Hypertext documentation of GLAM2 is available online at <ulink url="http://bioinformatics.org.au/glam2/">http://bioinformatics.org.au/glam2/</ulink> or on this computer in <filename class="directory">/usr/share/doc/glam2/</filename>.</para>
+ </refsect1>
+
+ <refsect1 id="ref">
+ <title>REFERENCE</title>
+ <para>
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+ </para>
+ </refsect1>
+</refentry>
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