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+.. 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?
+
+
--- /dev/null
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projects / mussa.git / commitdiff
