Brandon W. King
---------------
-Last updated: Oct 18th, 2006
+Last updated: Oct 20th, 2006
Updated to Mussagl build: (In process to 424)
See `Save Motifs to File`_ in the `Motifs`_ section.
+Viewing Multiple Analyses
+-------------------------
+
+Some times it is useful to view more than one analysis at a time. To
+do accomplish this, Mussa allows you to open a new Mussa window by
+selecting the **File > New Mussa Window** menu option.
+
+.. image:: images/new_mussa_window_menu.png
+ :alt: New Mussa Window Menu Option
+ :align: center
+
+A new Mussa window will pop up.
+
+.. figure:: images/new_mussa_window.png
+ :alt: New Mussa Window
+ :align: center
+
+ A new Mussa window on the right, in which a second analysis has
+ been loaded.
+
+Now you can create or load an existing analysis, in this new window,
+as described in the `Create/Load Analysis`_ section.
+
+You can view as many analyses as you can fit on your screen or until
+you run out of available RAM. If you notice a rapid decrease in
+performance and hear lots of noise coming from your hard drive, you
+probably ran out of RAM and are now using virtual memory (i.e. much
+much slower). If this happens, you may need to avoid opening as many
+analyses at one time.
+
+
Annotations / Motifs
--------------------
section. To save your motifs to a file, see the `save motifs to file`_
section.
+Deleting a Motif
+^^^^^^^^^^^^^^^^
+
+To delete a motif, remove all text from the name and sequence columns
+and close the motif editor.
View Mussa Alignments
---------------------
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
+NOT limited** to selecting only one subsequence from the same
sequence.
.. image:: images/subanalysis_select_seqs.png
:alt: Copy sequence
:align: center
+
Saving to an Image
---------------------------------
- * Updated to build 419.
-
To save your current mussa view to an image, select **File > Save to
image...** as shown below.
====== ================= ===================================
+
+Understanding Mussa
+===================
+
+
+Performance
+-----------
+
+Algorithm Behavior
+~~~~~~~~~~~~~~~~~~
+
+FIXME: Include seqcomp algorithm info.
+
+FIXME: Include transitivity info.
+
+Repeats
+~~~~~~~
+
+The algorithm Mussa uses to find conserved sequences is sensitive to
+repeated DNA segments, which are frequently occurring in most
+genomes. The problem with repeats, is that one repeat from one
+sequence can show up many times in another sequence. Every connection
+Mussa makes takes up memory and CPU time to process.
+
+The formula for the number of connections, C, that will be made for R
+instances of a single repeat (meaning R copies of one repeat in each
+sequence) and S sequences is:
+
+C = (R^2)[S(S-1)/2]
+
+Table of example situations:
+
+===== ===== =====
+ C R S
+===== ===== =====
+ 16 4 2
+ 48 4 3
+ 96 4 4
+ 160 4 5
+ 240 4 6
+ 336 4 7
+ 448 4 8
+ 24 2 4
+ 54 3 4
+ 96 4 4
+ 150 5 4
+ 216 6 4
+ 294 7 4
+ 384 8 4
+ 2500 50 2
+ 7500 50 3
+15000 50 4
+10000 100 2
+30000 100 3
+60000 100 4
+===== ===== =====
+
+After the connections, C, are found, they are passed on to the
+transitivity filter, which is a C^2 algorithm (FIXME: confirm
+algorithm is C^2). This means with 50 repeats in 2 sequences giving
+you a C of 2500, ends up with a C^2 of 6,250,000.
+
+**Conclusion: repeats cause the processing time of Mussa to skyrocket.**
+
+One way to deal with a situation where you have many repeats in your
+sequences is do any of the following: user shorter sequence lengths;
+repeat mask one or more of your sequences; or increase the threshold.
+
+Details
+-------
+
+Case: Conservation track suddenly stops
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+
.. Define links below
------------------