Brandon W. King
---------------
-Last updated: June 12th, 2006
+Last updated: July 7th, 2006
+
+Updated to Mussagl build: 287
+
+
+.. Things to add
+ * New features / change log
+ * Comment out anything isn't implemented yet.
+ * List of features that will be implemented in the future.
+ * Look into the homology mapping of UCSC.
+ * Add toggle to genomes.
+ * Document why one fast record per region.
+ * How to deal with the hazards of small utrs vis motif finder. (Add warning)
+ * Add warning about saving fasta file.
+ * Add a general principles section near the top
+ * Using comparison algorithm which will pickup all repeats
+ * Add info about repeatmasking
+ * Checking upstream and downstream genes for make sure you are in the right regions.
+ * Later on: look into Ensembl
+ * Look into method of homology instead of blating.
+ * Mention advantages of using mupa.
+ * Mention the difference between using arrows and scroll bar
+ * Document the color for motifs
+ * Update for Mac user left click
+
+* Wormbase/Flybase/mirBASE
-Updated to Mussagl build: 200 (Update to 230 in progress)
.. contents::
What is Mussagl?
----------------
+Mussa is an N-way version of the FamilyRelations (which is a part of
+the Cartwheel project) 2-way comparative sequence analysis
+software. Given DNA sequence from N species, Mussa uses all possible
+pairwise comparions to derive an N-wise comparison. For example, given
+sequences 1,2,3, and 4, Mussa makes 6 2-way comparisons: 1vs2, 1vs3,
+1vs4, 2vs3, 2vs4, and 3vs4. It then compares all the links between
+these comparisons, saving those that satisfy a transitivity
+requirement. The saved paths are then displayed in an interactive
+viewer.
Short History of Mussa
----------------------
Mussa Python/PMW Prototype
~~~~~~~~~~~~~~~~~~~~~~~~~~
+First Python/PMW based protoype.
Mussa C++/FLTK
~~~~~~~~~~~~~~
+A rewrite for speed purposes using C++ and FLTK GUI toolkit.
Mussagl C++/Qt/OpenGL
~~~~~~~~~~~~~~~~~~~~~
+Refactored version using the more elegant Qt GUI framework and
+OpenGL for hardware acceleration for those who have beter graphics
+cards.
Getting Mussagl
===============
(We only want to annotate CDS and UTRs.)
2. Select **one fasta record** per **region**.
(Mussa needs each CDS and UTR represented by one fasta record per CDS/UTR).
- 3. Select **split UTR and CDS parts of an exon into separate FASTA records**.
- (Breaks up **exons** into CDSs and UTRs.)
+ 3. Select **CDS in upper case, UTR in lower case.**
.. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png
:alt: Genome Browser - SMN1 (human) - Get genomic sequence setup
Motif Dialog
************
+**New Features:**
+
+Build 276
+ * Allow for toggling individual motifs on and off.
+
+Build 269
+ * Field added for naming motifs.
+
Mussa has the ability to find lab motifs using the `IUPAC Nucleotide
-Code`_ for defining a motif. To define a motif, select **View > Edit
+Code`_ for defining a motif. To define a motif, select **Edit > Edit
Motifs** menu item as shown below.
.. image:: images/view_edit_motifs.png
rows for defining motifs and the color that will be displayed on the
sequence. By default all 10 motifs start off as with white as the
color. In the image below, I changed the color from white to blue to
-make it easier to see.
+make it easier to see. The first text box is for the motif and the
+second box is for the name of the motif. The check box defines whether
+the motif is displayed or not.
.. image:: images/motif_dialog_start.png
:alt: Motif Dialog
:align: center
Now lets make a motif **'AT[C or G]CT'**. Using the `IUPAC Nucleotide
-Code`_, type in **'ATSCT'** into the first box as shown below.
+Code`_, type in **'ATSCT'** into the first box and 'My Motif' for the
+name in the second box as shown below.
.. image:: images/motif_dialog_enter_motif.png
:alt: Enter Motif
:align: center
+Sub-analysis
+------------
+
+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
+sequence.
+
+.. image:: images/subanalysis_select_seqs.png
+ :alt: Subanalysis sequence selection
+ :align: center
+
+Once you have added your sequences for subanalysis, choose a `window size`_ and `threshold`_ and click **Ok**.
+.. image:: images/subanalysis_dialog.png
+ :alt: Subanalysis Dialog
+ :align: center
+
+A new Mussa window will appear with the subanalysis of your sequences
+once it's done running. This may take a while if you selected large
+chunks of sequence with a loose threshold.
+
+.. image:: images/subanalysis_done.png
+ :alt: Subalaysis complete
+ :align: center
+
+
+Copying sequence to clipboard
+-----------------------------
+
+To copy a sequence to the clipboard, highlight a section of sequence,
+as shown in the screen shot below, and do one of the following:
+
+ * Select **Copy as Fasta** from the **Edit** menu.
+ * **Right Click (Left click + Apple/Command Key on Mac)** on the highlighted sequence and select **Copy as Fasta**.
+ * Press **Ctrl + C (on PC)** or **Apple/Command Key + C (on Mac)** on the keyboard.
+
+.. image:: images/copy_sequence.png
+ :alt: Copy sequence
+ :align: center
Saving to an Image
---------------------------------
projects / mussa.git / blobdiff