1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
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 "plessy@debian.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>converts GLAM2 motifs to FASTA or MSF format</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>
|
