Mussagl Manual: 1.0 docs part 4

[mussa.git] / doc / manual / mussagl_manual.rst

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index ed4642d9dccc273d2d3df9ea9d1f7b1bad2e0477..64dc7c4f1050397510040b5d4b6f784531185285 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -1,14 +1,11 @@
-==============
-Mussagl Manual
-==============
+===================
+Mussagl Manual v1.0
+===================
 ---------------
 Brandon W. King
 ---------------
 
-Last updated: Oct 27th, 2006
-
-Documentation for Mussagl v1.0
-
+Last updated: Oct 31st, 2006
 
 .. Things to add
        * New features / change log
@@ -39,17 +36,17 @@ Documentation for Mussagl v1.0
 Status
 ======
 
-Major New Features
-------------------
-
- * Build 381
-   * Analysis "Save As" feature
 
-Change Log
-----------
+..
 
-.. INSERT CHANGE LOG HERE
-.. END INSERT CHANGE LOG
+  .. Major New Features
+  .. ------------------
+  
+  .. Change Log
+  .. ----------
+  
+  .. INSERT CHANGE LOG HERE
+  .. END INSERT CHANGE LOG
 
 Features to be Implemented
 --------------------------
@@ -80,7 +77,7 @@ Short History of Mussa
 Mussa Python/PMW Prototype
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-First Python/PMW based protoype.
+First Python/PMW based prototype.
 
 Mussa C++/FLTK
 ~~~~~~~~~~~~~~
@@ -128,11 +125,11 @@ Install
 
 Mac OS X
 ~~~~~~~~
-Once you have downloaded the .dmg file, double click on it and follow
-the install instructions. 
-
-FIXME: Mention how to launch the program.
 
+ * Download .dmg file.
+ * Double click on .dmg file.
+ * Drag Mussa icon to your /Applications folder.
+ * Double Click on Mussa icon to open program.
 
 Windows XP
 ~~~~~~~~~~
@@ -269,13 +266,15 @@ open.
 
 If you would like to see an example, you can load the
 **mck3test.mupa** file in the examples directory that comes with
-Mussagl.
+Mussagl or read the `Step 5 - Create Analysis` section from the
+`Obtaining Input Data - Continued`_ section.
 
 .. image:: images/load_mupa_dialog.png
    :alt: Load Mussa Parameters Dialog
    :align: center
 
 
+
 Load an analysis
 ~~~~~~~~~~~~~~~~
 
@@ -378,6 +377,9 @@ between the sequences (i.e. not reverse complement matches)
 The amount of sequence conservation shown will depend on how much your
 sequences are related and the `dynamic threshold`_ you are using.
 
+To **deselect**, click and drag over any white area and then release
+the mouse button.
+
 
 Blue conservation tracks
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -395,6 +397,8 @@ to the sequence attached to the top of the blue line.
 The amount of sequence conservation shown will depend on how much your
 sequences are related and the `dynamic threshold`_ you are using.
 
+To **deselect**, click and drag over any white area and then release
+the mouse button.
 
 Zoom Factor
 ~~~~~~~~~~~
@@ -704,6 +708,10 @@ You should see the alignment at the base-pair level as shown below.
 Sub-analysis
 ------------
 
+Sub-analysis was created to allow you to analyze a sub-region using
+different parameters. This may allow you to find matches which may not
+have shown up with your initial settings.
+
 To run a sub-analysis **highlight** a section of sequence and *right
 click* on it and select **Add to subanalysis**. To the same for the
 sequences shown in orange in the screenshot below. Note that you **are
@@ -929,12 +937,16 @@ Motif File Format
 
 Format:
 
-  <motif> <red> <green> <blue>
+::
+
+  <motif> <optional name> <red> <green> <blue> <optional alpha>
   
 Example:
 
-  GGCC 0.0 1 1
+::
 
+  AGTGAG "My First Motif" 0.333333 0.588235 1 1
+  ATGAT "2nd Motif" 1 0 0 1
 
 
 IUPAC Nucleotide Code
@@ -987,7 +999,7 @@ The SMN1 data retrieved in this section can be downloaded from the
 you prefer to skip this section of the manual.
 
 UCSC Genome Browser Method
---------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 There are many methods of retrieving DNA sequence, but for this
 example we will retrieve SMN1 through the UCSC genome browser located
@@ -999,7 +1011,7 @@ at http://genome.ucsc.edu/.
    :align: center
 
 Step 1 - Find SMN1
-~~~~~~~~~~~~~~~~~~
+******************
 
 The first step in finding SMN1 is to use the **Gene Sorter** menu
 option which I have highlighted in orange below:
@@ -1050,7 +1062,7 @@ Now we have found the location of SMN1 on human!
 
 
 Step 2 - Download CDS/UTR sequence for annotations
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+**************************************************
 
 Since we have found **SMN1**, this would be a convenient time to extract
 the DNA sequence for the CDS and UTRs of the gene to use it as an
@@ -1136,7 +1148,7 @@ file. If found, it will be marked as an annotation_ within Mussa.
 
 
 Step 3 - Download gene and upstream/downstream sequence
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*******************************************************
 
 Use the back button in your web browser to get back the **genome
 browser view** of **SMN1** as shown below.
@@ -1181,7 +1193,7 @@ you find.
 
 
 Step 4 - Same/similar/related gene other species.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*************************************************
 
 What good is a multiple sequence alignment viewer without multiple
 sequences? Let'S find a similar gene in a few more species.
@@ -1269,7 +1281,7 @@ each one.
 
 
 Step 5 - Create Analysis
-~~~~~~~~~~~~~~~~~~~~~~~~
+************************
 
 At this point you should have the annotations and fasta files for each
 species. If you skipped the first four steps or are having trouble,