Presentation for bioinformatics club.

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--- a/doc/bioinfo_jc/bioinfo-presentation.rst
+++ b/doc/bioinfo_jc/bioinfo-presentation.rst
@@ -41,16 +41,63 @@ Family Tree
   
   .. _`Family Relations`: http://cartwheel.caltech.edu/
 
   
   .. _`Family Relations`: http://cartwheel.caltech.edu/
 

+Motivation
+----------
+
+.. class:: small
+
+  The hope is that conservation while highlight elements that are important.
+  However, it (by definition) only shows elements in common.
+
+  For instance though a two sequence comparision between a Human and Fugu 
+  muscle gene might show important elements of muscle, it would lose any
+  mammal specific elements. 
+
+  But a two sequence comparison between Mouse and Human might have too 
+  much in common to be useful.
+
+
+Motivation: Human vs. Fugu
+--------------------------
+
+.. class:: small
+
+  .. image:: HuFu.png
+
+Motivation: Human vs. Mouse
+---------------------------
+
+.. class:: small
+
+  .. image:: HuMo.png
+
+Motivation
+----------
+
+.. class:: small
+
+  The hope is that by requiring conservation in multiple more closely related
+  species one can achive the purification of the long distance comparison
+  while still allowing elements that are important to those more closely 
+  related species to remain.
+
+Motivation: Mammals
+-------------------
+
+.. class:: small
+
+  .. image:: HuCoDoMoRa.png
+

 Algorithm
 ---------
 
 .. class:: small
 
 Algorithm
 ---------
 
 .. class:: small
 

-  To compute a result Mussa conceptually uses these modules
-
-    * Seqcomp 
-    * Test Transitivity
-    * "Refinement"
+  To compute a result Mussa uses these algorithms to perform the N-way
+  filtering.
+  
+    * Seqcomp (determins the pairwise list of "matches")
+    * Transitivity Test (filters the matches)

 
 Seqcomp
 -------
 
 Seqcomp
 -------


@@ -67,11 +114,11 @@ Seqcomp
          match = 0
          for i in range(W):
            if S[0][x+i] == S[1][y+i]:
          match = 0
          for i in range(W):
            if S[0][x+i] == S[1][y+i]:

-             increment match 
-           if match > threshold: 
-             save indicies
+             match = match + 1
+           if match >= threshold: 
+             save_indicies(x,y)

 
 

-  The actual algorithm only needs to compare the base that 
+  The algorithm actully being used only needs to compare the base that 

   "slid in" into window, and account for the base that "slid out"
 
 Seqcomp
   "slid in" into window, and account for the base that "slid out"
 
 Seqcomp


@@ -83,7 +130,7 @@ Seqcomp
 
     .. image:: 4bp_window_no_match.png
 
 
     .. image:: 4bp_window_no_match.png
 

-  In this case there are none.
+  In this case there is only one.

 
 Seqcomp
 -------
 
 Seqcomp
 -------


@@ -94,7 +141,7 @@ Seqcomp
 
      .. image:: 4bp_window_match.png
 
 
      .. image:: 4bp_window_match.png
 

-   However, now that we slid over one position there are now 4
+   However, now that we slid over one position there are now 3

    and so we would record 0, 5
 
 Seqcomp
    and so we would record 0, 5
 
 Seqcomp


@@ -110,28 +157,174 @@ Seqcomp
 
      When extending to more than two sequences, mussa needs to compare
 
 
      When extending to more than two sequences, mussa needs to compare
 

-     (N * (N-1)) / 2 sequences
+     (N * (N-1)) sequences
+
+Transitivity Test
+-----------------
+
+.. class:: small
+
+  There are several algorithms for comparing multiple sequences.
+
+  * Require transitivity, e.g. if A = B, and B = C, then A = C
+  * "Radial" only tests matches between any number of query sequences
+    and a single reference sequence. A = B, A = C, but B ?= C
+  * "Entropy" (an experimental comparision that Tristan was working on)

 
 Test Transitivity
 -----------------
 
 
 Test Transitivity
 -----------------
 

-Refinement
-----------
+.. class:: small

 
 

+  .. image:: 4way_trans.png
+  
+  

 Limits
 ------
 
 Limits
 ------
 

-  describe the difference between a long distance comparison
-  and multiple closer comparisons. (should use some pictures for that)
+.. class:: small

 
 

-  paircomp/seqcomp
+  One of the weaknesses with the current implementation is that the
+  transitivity filtering step involves a combinatorial explosion as it 
+  compares every possible path.

 
 

-  transitivity filter
+  The parameters that influence the number of matches found are, 
+  repeat masking the sequence, how closely releated the two sequences
+  are, the length of the sequence and the stringency of the seqcomp 
+  threshold.

 
 

-How To Use
-----------
+Limits
+------

 
 

-  Should this include pulling things from the tutorial?
-  cover sucking things out of UCSC?
+.. class:: small
+
+  Additionally the types of elements found are influenced by the 
+  window size and base-pair threshold.
+
+  For instance a 6 base pair binding site wont be detected when using
+  a 30 base pair window size.
+
+Usage
+-----
+
+.. class:: small
+
+  Currently I have two classes of target user for mussa.
+
+    * Computationally savvy user (AKA me)
+    * The "typical" biologist (AKA my PI) 
+
+Tutorial
+--------
+
+  Brandon has been working on a tutorial for the GUI
+  which includes a section on how we extract sequence out of UCSC.
+
+
+Command-Line Features
+---------------------
+
+.. class:: small
+ 
+  * Command line::
+   
+      $ mussagl --help
+      --run-analysis  arg   run an analysis 
+                            defined by the mussa 
+                            parameter file
+      --view-analysis arg   load a previously run 
+                            analysis
+      --no-gui              terminate without viewing
+                            an analysis
+
+Command-Line Features
+---------------------
+
+.. class:: small
+
+   * Parameter file::
+
+       ANA_NAME mck3test
+       APPEND_WIN true
+       APPEND_THRES true
+
+       SEQUENCE seq/mouse_mck_pro.fa
+       ANNOTATION mm_mck3test.annot
+
+Command-Line Features
+---------------------
+
+.. class:: small
+
+  * Annotation File::
+
+      [Seq name]
+      start stop name type
+      >name
+      AGCGAAA
+
+  * [Seq name] is an optional name specifier.
+  * The "alignment" algorithm used for sequence specified annotations 
+    is currently just using the motif search, so it only accepts
+    IUPAC codes and doesn't handle in-dels.
+
+GUI Features
+------------
+
+.. class:: small
+
+   * The Create Analysis menu option provides the same options
+     as the parameter file.
+
+   .. image:: ../manual/images/define_analysis.png
+
+GUI Features
+------------
+
+.. class:: small
+
+   Although there isn't a GUI for describing large annotations.
+   (The motif editor can be used this way but there are issues).
+
+
+GUI Features
+------------
+
+.. class:: small
+
+   The Mussa GUI can:
+
+     * Display sequence with highlighted annotation regions
+     * Search for motifs in these sequences
+     * Show a base-pair alignment of a seqcomp "match"
+     * Copy sequence regions
+     * Create a new analysis using a subselection of one analysis
+       and different parameters.
+
+GUI
+---
+
+.. class:: small
+
+  <demo>
+
+Finish
+------
+
+.. class:: small
+
+Mussa has been developed by:
+
+  * Tristan DeBuysscher
+  * Diane Trout
+  * Brandon King
+  * Nora Mullaney

  
  

+And been influenced by:
+
+  * C. Titus Brown
+  * Erich Schwars
+  * and Barbara Wold

 
 

+  :tiny:`and as I stepped in fairly late in Mussa's life, there could easily 
+  be others.`