2 <assistantconfig version="3.2.0">
5 <property name="name">mussaglmanual</property>
6 <property name="title">Mussagl Manual</property>
7 <property name="applicationicon">images/handbook.png</property>
8 <property name="startpage">mussagl_manual.html</property>
9 <property name="aboutmenutext">About Mussagl Manual</property>
10 <property name="abouturl">about.txt</property>
11 <property name="assistantdocs">.</property>
14 <DCF ref="mussagl_manual.html" icon="handbook.png" imagedir="../img/"
15 title="Mussagl Manual">
17 <section ref="./mussagl_manual.html#contents" title="Contents" />
19 <section ref="./mussagl_manual.html#status" title="Status">
20 <section ref="./mussagl_manual.html#features-to-be-implemented" />
23 <section ref="./mussagl_manual.html#introduction" title="Introduction">
24 <section ref="./mussagl_manual.html#what-is-mussagl" title="What is Mussagl?">
25 <keyword ref="./mussagl_manual.html#what-is-mussagl">About</keyword>
27 <section ref="./mussagl_manual.html#short-history-of-mussa" title="Short History of Mussa">
28 <section ref="./mussagl_manual.html#mussa-python-pmw-prototype" title="Mussa Python/PMW Prototype"/>
29 <section ref="./mussagl_manual.html#mussa-c-fltk" title="Mussa C++/FLTK"/>
30 <section ref="./mussagl_manual.html#mussa-c-qt-opengl" title="Mussagl C++/Qt/OpenGL"/>
34 <section ref="./mussagl_manual.html#getting-mussagl" title="Getting Mussagl">
35 <section ref="./mussagl_manual.html#license" title="License"/>
36 <section ref="./mussagl_manual.html#platforms" title="Platforms"/>
37 <section ref="./mussagl_manual.html#download" title="Download"/>
39 <section ref="./mussagl_manual.html#install" title="Install">
40 <section ref="./mussagl_manual.html#mac-os-x" title="Mac OS X"/>
41 <section ref="./mussagl_manual.html#windows-xp" title="Windows XP"/>
42 <section ref="./mussagl_manual.html#linux" title="Linux"/>
43 <section ref="./mussagl_manual.html#build-from-source" title="Build from Source"/>
48 <section ref="./mussagl_manual.html#using-mussagl" title="Using Mussagl">
50 <section ref="./mussagl_manual.html#launch-mussagl" title="Launch Mussagl"/>
52 <section ref="./mussagl_manual.html#create-load-analysis" title="Create/Load Analysis">
53 <section ref="./mussagl_manual.html#create-a-new-analysis" title="Create a new analysis"/>
54 <section ref="./mussagl_manual.html#load-a-mussa-parameter-file" title="Load a mussa parameter file"/>
55 <section ref="./mussagl_manual.html#load-an-analysis" title="Load an analysis"/>
58 <section ref="./mussagl_manual.html#main-window" title="Main Window">
59 <section ref="./mussagl_manual.html#overview" title="Overview"/>
60 <section ref="./mussagl_manual.html#dna-sequence-black-bars" title="DNA Sequence (black bars)"/>
61 <section ref="./mussagl_manual.html#annotation" title="Annotation"/>
62 <section ref="./mussagl_manual.html#motif" title="Motif"/>
63 <section ref="./mussagl_manual.html#red-conservation-tracks" title="Red Conservation Tracks"/>
64 <section ref="./mussagl_manual.html#blue-conservation-tracks" title="Blue Conservation Tracks"/>
65 <section ref="./mussagl_manual.html#zoom-factor" title="Zoom Factor"/>
66 <section ref="./mussagl_manual.html#dynamic-threshold" title="Dynamic Threshold"/>
67 <section ref="./mussagl_manual.html#sequence-information-bar" title="Sequence Information Bar"/>
68 <section ref="./mussagl_manual.html#sequence-scroll-bar" title="Sequence Scroll Bar"/>
71 <section ref="./mussagl_manual.html#saving" title="Saving">
72 <section ref="./mussagl_manual.html#save-on-close" title="Save on close" />
73 <section ref="./mussagl_manual.html#save-analysis" title="Save Analysis" />
74 <section ref="./mussagl_manual.html#save-analysis-as" title="Save Analysis As" />
75 <section ref="./mussagl_manual.html#save-motif-list" title="Save Motif List" />
78 <section ref="./mussagl_manual.html#viewing-multiple-analyses" title="Viewing Multiple Analyses" />
81 <section ref="./mussagl_manual.html#annotations-motifs" title="Annotations / Motifs">
82 <section ref="./mussagl_manual.html#annotations" title="Annotations"/>
83 <section ref="./mussagl_manual.html#motifs" title="Motifs">
84 <section ref="./mussagl_manual.html#load-motifs-from-file" title="Load motifs from File"/>
85 <section ref="./mussagl_manual.html#save-motifs-to-file" title="Save Motifs to File"/>
86 <section ref="./mussagl_manual.html#motif-dialog" title="Motif Dialog">
87 <section ref="./mussagl_manual.html#deleting-a-motif" title="Deleting a Motif" />
93 <section ref="./mussagl_manual.html#view-mussa-alignments" title="View Mussa Alignments"/>
94 <section ref="./mussagl_manual.html#sub-analysis" title="Sub-analysis" />
95 <section ref="./mussagl_manual.html#copying-sequence-to-clipboard" title="Copying sequence to clipboard" />
97 <section ref="./mussagl_manual.html#saving-to-an-image" title="Saving to an Image"/>
99 <section ref="./mussagl_manual.html#detailed-information" title="Detailed Information">
100 <section ref="./mussagl_manual.html#threshold" title="Threshold"/>
101 <section ref="./mussagl_manual.html#window-size" title="Window Size"/>
102 <section ref="./mussagl_manual.html#sequences" title="Sequences"/>
105 <section ref="./mussagl_manual.html#mussa-file-formats" title="Mussa File Formats">
106 <section ref="./mussagl_manual.html#parameter-file-format" title="Parameter File Format"/>
107 <section ref="./mussagl_manual.html#annotation-file-format" title="Annotation File Format"/>
108 <section ref="./mussagl_manual.html#motif-file-format" title="Motif File Format"/>
109 <section ref="./mussagl_manual.html#iupac-necleotide-code" title="IUPAC Nucleotide Code"/>
112 <section ref="./mussagl_manual.html#obtaining-input-data-continued" title="Obtaining Input Data - Continued">
113 <section ref="./mussagl_manual.html#ucsc-genome-browser-method" title="UCSC Genome Browser Method" >
114 <section ref="./mussagl_manual.html#step-1-find-smn1" title="Step 1 - Find SMN1"/>
115 <section ref="./mussagl_manual.html#step-2-download-cds-utr-sequence-for-annotations" title="Step 2 - Download CDS/UTR sequence for annotations"/>
116 <section ref="./mussagl_manual.html#step-3-download-gene-and-upstream-downstream-sequence" title="Step 3 - Download gene and upstream/downstream sequence"/>
117 <section ref="./mussagl_manual.html#step-4-same-similar-related-gene-other-species" title="Step 4 - Same/similar/related gene other species."/>
118 <section ref="./mussagl_manual.html#step-5-create-analysis" title="Step 5 - Create Analysis"/>
123 <section ref="./mussagl_manual.html#understanding-mussa" title="Understanding Mussa"/>
124 <section ref="./mussagl_manual.html#command-line" title="Command Line"/>
125 <section ref="./mussagl_manual.html#performance" title="Performance">
126 <section ref="./mussagl_manual.html#algorithm-behavior" title="Algorithm Behavior"/>
127 <section ref="./mussagl_manual.html#repeats" title="Repeats"/>
129 <section ref="./mussagl_manual.html#details" title="Details">
130 <section ref="./mussagl_manual.html#case-conservation-track-suddenly-stops" title="Case: Conservation track suddenly stops"/>
132 <section ref="./mussagl_manual.html#python-interpreter" title="Python Interpreter"/>