From 58adf40f9b6e009f0d3d5fa2a277ad25ea63530d Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Sat, 8 Jul 2006 01:33:02 +0000
Subject: [PATCH] start of presentation for bioinformatics journal club 2006
 july 10

---
 doc/bioinfo_jc/4bp_window_match.png     | Bin 0 -> 4703 bytes
 doc/bioinfo_jc/4bp_window_match.svg     | 118 ++++++++
 doc/bioinfo_jc/4bp_window_no_match.png  | Bin 0 -> 4674 bytes
 doc/bioinfo_jc/4bp_window_no_match.svg  | 115 ++++++++
 doc/bioinfo_jc/bioinfo-presentation.rst | 137 +++++++++
 doc/bioinfo_jc/familytree.png           | Bin 0 -> 20072 bytes
 doc/bioinfo_jc/familytree.svg           | 374 ++++++++++++++++++++++++
 7 files changed, 744 insertions(+)
 create mode 100644 doc/bioinfo_jc/4bp_window_match.png
 create mode 100644 doc/bioinfo_jc/4bp_window_match.svg
 create mode 100644 doc/bioinfo_jc/4bp_window_no_match.png
 create mode 100644 doc/bioinfo_jc/4bp_window_no_match.svg
 create mode 100644 doc/bioinfo_jc/bioinfo-presentation.rst
 create mode 100644 doc/bioinfo_jc/familytree.png
 create mode 100644 doc/bioinfo_jc/familytree.svg

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diff --git a/doc/bioinfo_jc/bioinfo-presentation.rst b/doc/bioinfo_jc/bioinfo-presentation.rst
new file mode 100644
index 0000000..3437935
--- /dev/null
+++ b/doc/bioinfo_jc/bioinfo-presentation.rst
@@ -0,0 +1,137 @@
+.. include:: <s5defs.txt>
+
+=====
+Mussa
+=====
+
+:Authors: Diane Trout
+
+.. The contents of this directory contain the source
+   for a presentation for the Caltech Bioinformatics Journal club.
+
+.. footer:: Caltech Bioinformatics Journal Club
+
+What is Mussa
+-------------
+
+.. class:: small 
+
+  Mussa is tool to search for conserved regions between several
+  sequences. Hopefully regions detected as conserved will 
+  highlight potentially important DNA sequence features such as
+  cis-regulatory modules, microRNA genes, and exons.
+
+  Mussa extends previous 2-way sequence comparison to N sequences. 
+
+Family Tree
+-----------
+
+.. class:: small 
+
+  Family Relations and Mussa started using the same sequence
+  comparison algorithm but developed in different directions.
+
+    .. image:: familytree.png
+        :alt: Gratutious software family tree
+
+  `Family Relations`_ focused on providing a robust usable piece
+  of software.
+
+  Mussa focused on the N-way algorithm.
+  
+  .. _`Family Relations`: http://cartwheel.caltech.edu/
+
+Algorithm
+---------
+
+.. class:: small
+
+  To compute a result Mussa conceptually uses these modules
+
+    * Seqcomp 
+    * Test Transitivity
+    * "Refinement"
+
+Seqcomp
+-------
+
+.. class:: small
+
+  The original seqcomp comparion uses a refinement of a fairly simple 
+  algorithm to compare two sequences.
+
+  Given window of size W and sequences S[0] and S[1]::
+     
+     for x in range(len(S[0])-W):
+       for y in range(len(S[1])-W):
+         match = 0
+         for i in range(W):
+           if S[0][x+i] == S[1][y+i]:
+             increment match 
+           if match > threshold: 
+             save indicies
+
+  The actual algorithm only needs to compare the base that 
+  "slid in" into window, and account for the base that "slid out"
+
+Seqcomp
+-------
+
+.. class:: small
+
+  Assume that in this case we need 3 matches out of 4
+
+    .. image:: 4bp_window_no_match.png
+
+  In this case there are none.
+
+Seqcomp
+-------
+
+.. class:: small
+
+   Assume that in this case we need 3 matches out of 4
+
+     .. image:: 4bp_window_match.png
+
+   However, now that we slid over one position there are now 4
+   and so we would record 0, 5
+
+Seqcomp
+-------
+
+.. class:: small
+
+
+  Once one pass is complete one of the sequences is reversed complimented
+  and the process is repeated.
+
+  .. container:: incremental
+
+     When extending to more than two sequences, mussa needs to compare
+
+     (N * (N-1)) / 2 sequences
+
+Test Transitivity
+-----------------
+
+Refinement
+----------
+
+Limits
+------
+
+  describe the difference between a long distance comparison
+  and multiple closer comparisons. (should use some pictures for that)
+
+  paircomp/seqcomp
+
+  transitivity filter
+
+How To Use
+----------
+
+  Should this include pulling things from the tutorial?
+  cover sucking things out of UCSC?
+ 
+
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-- 
2.30.2