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[mussa.git] / doc / manual / mussagl_manual.qhp
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13             <section ref="./mussagl_manual.html#contents" title="Contents" />
14             <section ref="./mussagl_manual.html#status" title="Status">
15                 <section ref="./mussagl_manual.html#features-to-be-implemented" />
16             </section>
17             <section ref="./mussagl_manual.html#introduction" title="Introduction">
18                 <section ref="./mussagl_manual.html#what-is-mussagl" title="What is Mussagl?">
19                     <section ref="./mussagl_manual.html#what-is-mussagl">About</section>
20                 </section>
21                 <section ref="./mussagl_manual.html#short-history-of-mussa" title="Short History of Mussa">
22                     <section ref="./mussagl_manual.html#mussa-python-pmw-prototype" title="Mussa Python/PMW Prototype"/>
23                     <section ref="./mussagl_manual.html#mussa-c-fltk" title="Mussa C++/FLTK"/>
24                     <section ref="./mussagl_manual.html#mussa-c-qt-opengl" title="Mussagl C++/Qt/OpenGL"/>
25                 </section>
26             </section>
27             <section ref="./mussagl_manual.html#getting-mussagl" title="Getting Mussagl">
28                 <section ref="./mussagl_manual.html#license" title="License"/>
29                 <section ref="./mussagl_manual.html#platforms" title="Platforms"/>
30                 <section ref="./mussagl_manual.html#download" title="Download"/>
31                 <section ref="./mussagl_manual.html#install" title="Install">
32                   <section ref="./mussagl_manual.html#mac-os-x" title="Mac OS X"/>
33                   <section ref="./mussagl_manual.html#windows-xp" title="Windows XP"/>
34                   <section ref="./mussagl_manual.html#linux" title="Linux"/>
35                   <section ref="./mussagl_manual.html#build-from-source" title="Build from Source"/>
36                 </section>
37             </section>
38             <section ref="./mussagl_manual.html#using-mussagl" title="Using Mussagl">
39                 <section ref="./mussagl_manual.html#launch-mussagl" title="Launch Mussagl"/>
40                 <section ref="./mussagl_manual.html#create-load-analysis" title="Create/Load Analysis">
41                   <section ref="./mussagl_manual.html#create-a-new-analysis" title="Create a new analysis"/>
42                   <section ref="./mussagl_manual.html#load-a-mussa-parameter-file" title="Load a mussa parameter file"/>
43                   <section ref="./mussagl_manual.html#load-an-analysis" title="Load an analysis"/>
44                 </section>
45                 <section ref="./mussagl_manual.html#main-window" title="Main Window">
46                   <section ref="./mussagl_manual.html#overview" title="Overview"/>
47                   <section ref="./mussagl_manual.html#dna-sequence-black-bars" title="DNA Sequence (black bars)"/>
48                   <section ref="./mussagl_manual.html#annotation" title="Annotation"/>
49                   <section ref="./mussagl_manual.html#motif" title="Motif"/>
50                   <section ref="./mussagl_manual.html#red-conservation-tracks" title="Red Conservation Tracks"/>
51                   <section ref="./mussagl_manual.html#blue-conservation-tracks" title="Blue Conservation Tracks"/>
52                   <section ref="./mussagl_manual.html#zoom-factor" title="Zoom Factor"/>
53                   <section ref="./mussagl_manual.html#dynamic-threshold" title="Dynamic Threshold"/>
54                   <section ref="./mussagl_manual.html#sequence-information-bar" title="Sequence Information Bar"/>
55                   <section ref="./mussagl_manual.html#sequence-scroll-bar" title="Sequence Scroll Bar"/>
56                 </section>
57                 <section ref="./mussagl_manual.html#saving" title="Saving">
58                   <section ref="./mussagl_manual.html#save-on-close" title="Save on close" />
59                   <section ref="./mussagl_manual.html#save-analysis" title="Save Analysis" />
60                   <section ref="./mussagl_manual.html#save-analysis-as" title="Save Analysis As" />
61                   <section ref="./mussagl_manual.html#save-motif-list" title="Save Motif List" />
62                 </section>
63                 <section ref="./mussagl_manual.html#viewing-multiple-analyses" title="Viewing Multiple Analyses" />
64                 <section ref="./mussagl_manual.html#annotations-motifs" title="Annotations / Motifs">
65                   <section ref="./mussagl_manual.html#annotations" title="Annotations"/>
66                   <section ref="./mussagl_manual.html#motifs" title="Motifs">
67                     <section ref="./mussagl_manual.html#load-motifs-from-file" title="Load motifs from File"/>
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69                     <section ref="./mussagl_manual.html#motif-dialog" title="Motif Dialog">
70                         <section ref="./mussagl_manual.html#deleting-a-motif" title="Deleting a Motif" />
71                     </section>
72                   </section> 
73                 </section>              
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75                 <section ref="./mussagl_manual.html#sub-analysis" title="Sub-analysis" />
76                 <section ref="./mussagl_manual.html#copying-sequence-to-clipboard" title="Copying sequence to clipboard" />
77                 <section ref="./mussagl_manual.html#saving-to-an-image" title="Saving to an Image"/>
78                 <section ref="./mussagl_manual.html#detailed-information" title="Detailed Information">
79                   <section ref="./mussagl_manual.html#threshold" title="Threshold"/>
80                   <section ref="./mussagl_manual.html#window-size" title="Window Size"/>
81                   <section ref="./mussagl_manual.html#sequences" title="Sequences"/>
82                 </section>
83                 <section ref="./mussagl_manual.html#mussa-file-formats" title="Mussa File Formats">
84                   <section ref="./mussagl_manual.html#parameter-file-format" title="Parameter File Format"/>
85                   <section ref="./mussagl_manual.html#annotation-file-format" title="Annotation File Format"/>
86                   <section ref="./mussagl_manual.html#motif-file-format" title="Motif File Format"/>
87                   <section ref="./mussagl_manual.html#iupac-necleotide-code" title="IUPAC Nucleotide Code"/>
88                 </section>
89                 <section ref="./mussagl_manual.html#obtaining-input-data-continued" title="Obtaining Input Data - Continued">
90                         <section ref="./mussagl_manual.html#ucsc-genome-browser-method" title="UCSC Genome Browser Method" >
91                                 <section ref="./mussagl_manual.html#step-1-find-smn1" title="Step 1 - Find SMN1"/>
92                                 <section ref="./mussagl_manual.html#step-2-download-cds-utr-sequence-for-annotations" title="Step 2 - Download CDS/UTR sequence for annotations"/>
93                                 <section ref="./mussagl_manual.html#step-3-download-gene-and-upstream-downstream-sequence" title="Step 3 - Download gene and upstream/downstream sequence"/>
94                                 <section ref="./mussagl_manual.html#step-4-same-similar-related-gene-other-species" title="Step 4 - Same/similar/related gene other species."/>
95                                 <section ref="./mussagl_manual.html#step-5-create-analysis" title="Step 5 - Create Analysis"/>
96                         </section>
97                 </section>
98                  <section ref="./mussagl_manual.html#understanding-mussa" title="Understanding Mussa"/>
99                          <section ref="./mussagl_manual.html#command-line" title="Command Line"/>
100                          <section ref="./mussagl_manual.html#performance" title="Performance">
101                                  <section ref="./mussagl_manual.html#algorithm-behavior" title="Algorithm Behavior"/>
102                                  <section ref="./mussagl_manual.html#repeats" title="Repeats"/>
103                          </section>
104                          <section ref="./mussagl_manual.html#details" title="Details">
105                                  <section ref="./mussagl_manual.html#case-conservation-track-suddenly-stops" title="Case: Conservation track suddenly stops"/>
106                          </section>
107                          <section ref="./mussagl_manual.html#python-interpreter" title="Python Interpreter"/>
108                 </section>
109          </toc>
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