Conservation tracks + IUPAC Neucleotide Table

 * Added information about conservation tracks, and the meaning of
   blue vs red track.

 * Added an IUPAC Neucleotide Table

diff --git a/doc/manual/images/conservation_tracks.png b/doc/manual/images/conservation_tracks.png
index 999c44fe400c056ec6f0584f49dfd37762092ad9..6c001c5d12dd81df932c19d5935d60ba0acde4d4 100644 (file)
Binary files a/doc/manual/images/conservation_tracks.png and b/doc/manual/images/conservation_tracks.png differ

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 615160444f2e896929ec0aba52bdedd692dc7086..3f46aaa3d29f572da0404c4023c6481d466285e6 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -302,13 +302,15 @@ Conservation tracks
    :alt: Conservation Tracks
    :align: center
    
-   Conservations tracks shown as red lines between sequence bars.
+   Conservations tracks shown as red and blue lines between sequence
+   bars.
 
-The red lines between the sequence bars represent conservation between
-the sequences. The amount of sequence conservation shown will depend
-on the relatedness of your sequences and the `dynamic threshold` you
-are using. Sequences with lots of repeats will cause major slow downs
-in calculating the matches.
+The **red lines** between the sequence bars represent conservation
+between the sequences and **blue lines** represent **reverse
+complement** conservation. The amount of sequence conservation shown
+will depend on the relatedness of your sequences and the `dynamic
+threshold` you are using. Sequences with lots of repeats will cause
+major slow downs in calculating the matches.
 
 
 Motif Toggle
@@ -420,7 +422,22 @@ Note: Currently not implemented
 Motif Dialog
 ************
 
-FIXME: Continue here.
+Mussa has the ability to find lab motifs using the `IUPAC Nucleotide
+Code`_ for defining a motif. To define a motif, select **View > Edit
+Motifs** menu item as shown below.
+
+.. image:: images/view_edit_motifs.png
+   :alt: "View > Edit Motifs" Menu
+   :align: center
+
+You will see a dialog box appear with a "set motifs" button and 10
+rows for defining motifs and the color that will be displayed on the
+sequence. By default all 10 motifs start off as with white as the color.
+
+.. image:: images/motif_dialog_start.png
+   :alt: Motif Dialog
+   :align: center
+
 
 Detailed Info
 -------------
@@ -583,6 +600,37 @@ Example:
   GGCC 0.0 1 1
 
 
+
+IUPAC Nucleotide Code
+~~~~~~~~~~~~~~~~~~~~~
+
+For your convience, below is a table of the IUPAC Nucleotide Code.
+
+The following table is table 1 from "Nomenclature for Incompletely
+Specified Bases in Nucleic Acid Sequences" which can be found at
+http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html.
+
+======  =================  ===================================
+Symbol Meaning            Origin of designation
+======  =================  ===================================
+G      G                  Guanine
+A      A                  Adenine
+T      T                  Thymine
+C      C                  Cytosine
+R      G or A             puRine
+Y      T or C             pYrimidine
+M      A or C             aMino
+K      G or T             Keto
+S      G or C             Strong interaction (3 H bonds)
+W      A or T             Weak interaction (2 H bonds)
+H      A or C or T        not-G, H follows G in the alphabet
+B      G or T or C        not-A, B follows A
+V      G or C or A        not-T (not-U), V follows U
+D      G or A or T        not-C, D follows C
+N      G or A or T or C   aNy
+======  =================  ===================================
+
+
 .. Define links below
    ------------------