Manual: UCSC Update, Copy sequence, Sub-analysis

 * Added more screenshots
 * Updated UCSC Genome Browser sequence retrieval information
 * Copy sequence to clipboard section added
 * Subanalysis section added

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diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index f81d689d22ce6d0563a92a6ad1bf58b1c19bcbf6..273e65a99899a71ff3e16259f5e29e6c6c58812d 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -5,9 +5,9 @@ Mussagl Manual
 Brandon W. King
 ---------------
 
-Last updated: June 12th, 2006
+Last updated: July 7th, 2006
 
-Updated to Mussagl build: 200 (Update to 230 in progress)
+Updated to Mussagl build: 200 (Update to 286 in progress)
 
 
 .. contents::
@@ -19,6 +19,15 @@ Introduction
 What is Mussagl?
 ----------------
 
+Mussa is an N-way version of the FamilyRelations (which is a part of
+the Cartwheel project) 2-way comparative sequence analysis
+software. Given DNA sequence from N species, Mussa uses all possible
+pairwise comparions to derive an N-wise comparison. For example, given
+sequences 1,2,3, and 4, Mussa makes 6 2-way comparisons: 1vs2, 1vs3,
+1vs4, 2vs3, 2vs4, and 3vs4. It then compares all the links between
+these comparisons, saving those that satisfy a transitivity
+requirement. The saved paths are then displayed in an interactive
+viewer.
 
 Short History of Mussa
 ----------------------
@@ -27,14 +36,19 @@ Short History of Mussa
 Mussa Python/PMW Prototype
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+First Python/PMW based protoype.
 
 Mussa C++/FLTK
 ~~~~~~~~~~~~~~
 
+A rewrite for speed purposes using C++ and FLTK GUI toolkit.
 
 Mussagl C++/Qt/OpenGL
 ~~~~~~~~~~~~~~~~~~~~~
 
+Refactored version using the more elegant Qt GUI framework and
+OpenGL for hardware acceleration for those who have beter graphics
+cards.
 
 Getting Mussagl
 ===============
@@ -217,8 +231,7 @@ below):
     (We only want to annotate CDS and UTRs.)
  2. Select **one fasta record** per **region**. 
     (Mussa needs each CDS and UTR represented by one fasta record per CDS/UTR).
- 3. Select **split UTR and CDS parts of an exon into separate FASTA records**.
-    (Breaks up **exons** into CDSs and UTRs.)
+ 3. Select **CDS in upper case, UTR in lower case.**
 
 .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png
    :alt: Genome Browser - SMN1 (human) - Get genomic sequence setup
@@ -808,7 +821,47 @@ You should see the alignment at the base-pair level as shown below.
    :align: center
 
 
+Sub-analysis
+------------
 
+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
+NOT limited** to selecting more than one subsequence from the same
+sequence.
+
+.. image:: images/subanalysis_select_seqs.png
+   :alt: Subanalysis sequence selection
+   :align: center
+
+Once you have added your sequences for subanalysis, choose a `window size`_ and `threshold`_ and click **Ok**.
+
+.. image:: images/subanalysis_dialog.png
+   :alt: Subanalysis Dialog
+   :align: center
+
+A new Mussa window will appear with the subanalysis of your sequences
+once it's done running. This may take a while if you selected large
+chunks of sequence with a loose threshold.
+
+.. image:: images/subanalysis_done.png
+   :alt: Subalaysis complete
+   :align: center
+
+
+Copying sequence to clipboard
+-----------------------------
+
+To copy a sequence to the clipboard, highlight a section of sequence,
+as shown in the screen shot below, and do one of the following:
+
+ * Select **Copy as Fasta** from the **Edit** menu.
+ * **Right Click (Left click + Apple/Command Key on Mac)** on the highlighted sequence and select **Copy as Fasta**.
+ * Press **Ctrl + C (on PC)** or **Apple/Command Key + C (on Mac)** on the keyboard.
+
+.. image:: images/copy_sequence.png
+   :alt: Copy sequence
+   :align: center
 
 Saving to an Image
 ---------------------------------