* Updated all images in overview section to latest version of Mussa. (Tickets: #166, #172, #173)
* Updated text in section to match latest version of Mussa. (Tickets: #166, #172, #173)
* Removed 'Motif Toggle' button documentation. (ticket:171)
For more information about SMN1 visit `NCBI's OMIM
<http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=609682>`_.
For more information about SMN1 visit `NCBI's OMIM
<http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=609682>`_.
+The SMN1 data retrieved in this section can be downloaded from the
+`Mussa Example Data
+<http://woldlab.caltech.edu/cgi-bin/mussa/wiki/ExampleData>`_ page if
+you prefer to skip this section of the manual.
+
+
UCSC Genome Browser Method
--------------------------
UCSC Genome Browser Method
--------------------------
example we will retrieve SMN1 through the UCSC genome browser located
at http://genome.ucsc.edu/.
example we will retrieve SMN1 through the UCSC genome browser located
at http://genome.ucsc.edu/.
-We have made the SMN1 data available at
-http://woldlab.caltech.edu/cgi-bin/mussa/wiki/ExampleData if you
-prefer to skip this section.
.. image:: images/ucsc_genome_browser_home.png
:alt: UCSC Genome Browser
.. image:: images/ucsc_genome_browser_home.png
:alt: UCSC Genome Browser
- 4. `Conservation tracks`_
+ 4. `Red conservation tracks`_
+ 5. `Blue conservation tracks`_
6. `Zoom Factor`_ (Base pairs per pixel)
6. `Zoom Factor`_ (Base pairs per pixel)
Each of the black bars represents one of the loaded sequences, in this
case the sequence around the gene 'MCK' in human, mouse, and rabbit.
Each of the black bars represents one of the loaded sequences, in this
case the sequence around the gene 'MCK' in human, mouse, and rabbit.
-FIXME: Should I mention the repeats here?
-
Annotations can be included on any of the sequences using the `Load a
Annotations can be included on any of the sequences using the `Load a
-mussa parameter file`_ method of loading your sequences. You can
-define annotations by location or using an exact sub-sequence and you
-may also choose any color for display of the annotation; see the
-`Annotation File Format`_ section for details.
-
-Note: Currently there is no way to add annotations using the GUI (only
-via the .mupa file). We plan to add this feature in the future, but it
-likely will not make it into the first release.
+mussa parameter file`_ or `Create a new analysis`_ method of loading
+your sequences. You can define annotations by location or using an
+exact sub-sequence or a FASTA sequence of the section of DNA you wish
+to annotate. See the `Annotation File Format`_ section for details.
Motif shown in light blue on sequence bar.
The only real difference between an annotation and motif in Mussagl is
Motif shown in light blue on sequence bar.
The only real difference between an annotation and motif in Mussagl is
-that you can define motifs from within the GUI. See the `Motifs`_
-section for more information.
+that you can define motifs and choose a color from within the GUI. See
+the `Motifs`_ section for more information.
-Conservation tracks
-~~~~~~~~~~~~~~~~~~~
+Red conservation tracks
+~~~~~~~~~~~~~~~~~~~~~~~
.. figure:: images/conservation_tracks.png
:alt: Conservation Tracks
.. figure:: images/conservation_tracks.png
:alt: Conservation Tracks
bars.
The **red lines** between the sequence bars represent conservation
bars.
The **red lines** between the sequence bars represent conservation
-between the sequences and **blue lines** represent **reverse
-complement** conservation. The amount of sequence conservation shown
-will depend on the relatedness of your sequences and the `dynamic
-threshold` you are using. Sequences with lots of repeats will cause
-major slow downs in calculating the matches.
+between the sequences (i.e. not reverse complement matches)
+
+The amount of sequence conservation shown will depend on how much your
+sequences are related and the `dynamic threshold`_ you are using.
-Motif Toggle
-~~~~~~~~~~~~
+Blue conservation tracks
+~~~~~~~~~~~~~~~~~~~~~~~~
-.. image:: images/motif_toggle.png
- :alt: Motif Toggle
+.. figure:: images/conservation_tracks.png
+ :alt: Conservation Tracks
+
+ Conservations tracks shown as red and blue lines between sequence
+ bars.
-Toggles motifs on and off. This will not turn on and off annotations.
+**Blue lines** represent **reverse complement** conservation relative
+to the sequence attached to the top of the blue line.
-Note: As of the current build (#200), this feature hasn't been
-implemented.
+The amount of sequence conservation shown will depend on how much your
+sequences are related and the `dynamic threshold`_ you are using.
:align: center
You can dynamically change the threshold for how strong a match you
:align: center
You can dynamically change the threshold for how strong a match you
-consider the conservation to be with one of two options:
+consider the conservation to be by changing the value in the dynamic
+threshold box.
- 1. Number of base pair matches out of window size.
-
- 2. Percent base pair conservation.
+The value you enter is the minimum number of base pairs that have to
+be matched in order to be considered conserved. The second number that
+you can't change is the `window size`_ you used when creating the
+experiment. The last number is the percent match.
See the Threshold_ section for more information.
See the Threshold_ section for more information.
2. Total Size of Sequence
3. Current base pair position
2. Total Size of Sequence
3. Current base pair position
+Note that you can **update the species** text box. Make sure to **save your
+experiment** after making this change by selecting **File > Save
+Analysis** from the menu.
Sequence Scroll Bar
~~~~~~~~~~~~~~~~~~~
Sequence Scroll Bar
~~~~~~~~~~~~~~~~~~~
projects / mussa.git / commitdiff
