Mussa manual: Overview section update

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

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 5bd26d4188d989d768124240557fa34e925ed3ea..949a424f4dea77729101fa9992d57a9aa6a43085 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -178,6 +178,12 @@ DNA sequence for SMN1 and prepare it for using in Mussa.
 For more information about SMN1 visit `NCBI's OMIM
 <http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=609682>`_.
 
+The SMN1 data retrieved in this section can be downloaded from the
+`Mussa Example Data
+<http://woldlab.caltech.edu/cgi-bin/mussa/wiki/ExampleData>`_ page if
+you prefer to skip this section of the manual.
+
+
 UCSC Genome Browser Method
 --------------------------
 
@@ -185,9 +191,6 @@ There are many methods of retrieving DNA sequence, but for this
 example we will retrieve SMN1 through the UCSC genome browser located
 at http://genome.ucsc.edu/.
 
-We have made the SMN1 data available at
-http://woldlab.caltech.edu/cgi-bin/mussa/wiki/ExampleData if you
-prefer to skip this section.
 
 .. image:: images/ucsc_genome_browser_home.png
    :alt: UCSC Genome Browser
@@ -595,9 +598,9 @@ Legend:
 
  3. Motif_
 
- 4. `Conservation tracks`_
+ 4. `Red conservation tracks`_
 
- 5. `Motif Toggle`_
+ 5. `Blue conservation tracks`_
 
  6. `Zoom Factor`_ (Base pairs per pixel)
 
@@ -618,8 +621,6 @@ DNA Sequence (black bars)
 Each of the black bars represents one of the loaded sequences, in this
 case the sequence around the gene 'MCK' in human, mouse, and rabbit.
 
-FIXME: Should I mention the repeats here?
-
 
 Annotation
 ~~~~~~~~~~
@@ -632,14 +633,10 @@ Annotation
 
 
 Annotations can be included on any of the sequences using the `Load a
-mussa parameter file`_ method of loading your sequences. You can
-define annotations by location or using an exact sub-sequence and you
-may also choose any color for display of the annotation; see the
-`Annotation File Format`_ section for details.
-
-Note: Currently there is no way to add annotations using the GUI (only
-via the .mupa file). We plan to add this feature in the future, but it
-likely will not make it into the first release.
+mussa parameter file`_ or `Create a new analysis`_ method of loading
+your sequences. You can define annotations by location or using an
+exact sub-sequence or a FASTA sequence of the section of DNA you wish
+to annotate. See the `Annotation File Format`_ section for details.
 
 
 Motif
@@ -652,12 +649,12 @@ Motif
    Motif shown in light blue on sequence bar.
 
 The only real difference between an annotation and motif in Mussagl is
-that you can define motifs from within the GUI. See the `Motifs`_
-section for more information.
+that you can define motifs and choose a color from within the GUI. See
+the `Motifs`_ section for more information.
 
 
-Conservation tracks
-~~~~~~~~~~~~~~~~~~~
+Red conservation tracks
+~~~~~~~~~~~~~~~~~~~~~~~
 
 .. figure:: images/conservation_tracks.png
    :alt: Conservation Tracks
@@ -667,24 +664,27 @@ Conservation tracks
    bars.
 
 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.
+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.
 
 
-Motif Toggle
-~~~~~~~~~~~~
+Blue conservation tracks
+~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. image:: images/motif_toggle.png
-   :alt: Motif Toggle
+.. figure:: images/conservation_tracks.png
+   :alt: Conservation Tracks
    :align: center
+   
+   Conservations tracks shown as red and blue lines between sequence
+   bars.
 
-Toggles motifs on and off. This will not turn on and off annotations.
+**Blue lines** represent **reverse complement** conservation relative
+to the sequence attached to the top of the blue line.
 
-Note: As of the current build (#200), this feature hasn't been
-implemented.
+The amount of sequence conservation shown will depend on how much your
+sequences are related and the `dynamic threshold`_ you are using.
 
 
 Zoom Factor
@@ -708,11 +708,13 @@ Dynamic Threshold
    :align: center
 
 You can dynamically change the threshold for how strong a match you
-consider the conservation to be with one of two options:
+consider the conservation to be by changing the value in the dynamic
+threshold box. 
 
- 1. Number of base pair matches out of window size.
- 
- 2. Percent base pair conservation.
+The value you enter is the minimum number of base pairs that have to
+be matched in order to be considered conserved. The second number that
+you can't change is the `window size`_ you used when creating the
+experiment. The last number is the percent match.
 
 See the Threshold_ section for more information.
 
@@ -732,6 +734,9 @@ information:
  2. Total Size of Sequence
  3. Current base pair position
 
+Note that you can **update the species** text box. Make sure to **save your
+experiment** after making this change by selecting **File > Save
+Analysis** from the menu.
 
 Sequence Scroll Bar
 ~~~~~~~~~~~~~~~~~~~