From: Brandon King <kingb@caltech.edu>
Date: Tue, 23 May 2006 18:06:31 +0000 (+0000)
Subject: Conservation tracks + IUPAC Neucleotide Table
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=87e164affe345f81758ecaa6289b8f3351e859d8

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 999c44f..6c001c5 100644
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 6151604..3f46aaa 100644
--- 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
    ------------------