From: Brandon King Date: Mon, 16 Oct 2006 18:51:19 +0000 (+0000) Subject: Mussa manual: Overview section update X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=b9ad8845732c9bb6a151509163961a03befe3de4 Mussa manual: Overview section update * 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) --- diff --git a/doc/manual/images/annotation.png b/doc/manual/images/annotation.png index 8f10078..9dc6770 100644 Binary files a/doc/manual/images/annotation.png and b/doc/manual/images/annotation.png differ diff --git a/doc/manual/images/conservation_tracks.png b/doc/manual/images/conservation_tracks.png index 6c001c5..6bcb96a 100644 Binary files a/doc/manual/images/conservation_tracks.png and b/doc/manual/images/conservation_tracks.png differ diff --git a/doc/manual/images/dynamic_threshold.png b/doc/manual/images/dynamic_threshold.png index bd810cd..6e551f5 100644 Binary files a/doc/manual/images/dynamic_threshold.png and b/doc/manual/images/dynamic_threshold.png differ diff --git a/doc/manual/images/motif.png b/doc/manual/images/motif.png index a2b73b9..c9e34e7 100644 Binary files a/doc/manual/images/motif.png and b/doc/manual/images/motif.png differ diff --git a/doc/manual/images/scroll_bar.png b/doc/manual/images/scroll_bar.png index 69f3e95..9626d4c 100644 Binary files a/doc/manual/images/scroll_bar.png and b/doc/manual/images/scroll_bar.png differ diff --git a/doc/manual/images/seq_info_bar.png b/doc/manual/images/seq_info_bar.png index 854c744..71f5823 100644 Binary files a/doc/manual/images/seq_info_bar.png and b/doc/manual/images/seq_info_bar.png differ diff --git a/doc/manual/images/sequence_bar.png b/doc/manual/images/sequence_bar.png index a76f690..1c4982a 100644 Binary files a/doc/manual/images/sequence_bar.png and b/doc/manual/images/sequence_bar.png differ diff --git a/doc/manual/images/window_overview.png b/doc/manual/images/window_overview.png index 189643e..4a34a92 100644 Binary files a/doc/manual/images/window_overview.png and b/doc/manual/images/window_overview.png differ diff --git a/doc/manual/images/window_overview.xcf b/doc/manual/images/window_overview.xcf index d6a46e2..1d97dd6 100644 Binary files a/doc/manual/images/window_overview.xcf and b/doc/manual/images/window_overview.xcf differ diff --git a/doc/manual/images/zoom_factor.png b/doc/manual/images/zoom_factor.png index fe2af8a..f1a096f 100644 Binary files a/doc/manual/images/zoom_factor.png and b/doc/manual/images/zoom_factor.png differ diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index 5bd26d4..949a424 100644 --- a/doc/manual/mussagl_manual.rst +++ b/doc/manual/mussagl_manual.rst @@ -178,6 +178,12 @@ DNA sequence for SMN1 and prepare it for using in Mussa. For more information about SMN1 visit `NCBI's OMIM `_. +The SMN1 data retrieved in this section can be downloaded from the +`Mussa Example Data +`_ page if +you prefer to skip this section of the manual. + + UCSC Genome Browser Method -------------------------- @@ -185,9 +191,6 @@ There are many methods of retrieving DNA sequence, but for this 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 @@ -595,9 +598,9 @@ Legend: 3. Motif_ - 4. `Conservation tracks`_ + 4. `Red conservation tracks`_ - 5. `Motif Toggle`_ + 5. `Blue conservation tracks`_ 6. `Zoom Factor`_ (Base pairs per pixel) @@ -618,8 +621,6 @@ DNA Sequence (black bars) 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? - Annotation ~~~~~~~~~~ @@ -632,14 +633,10 @@ Annotation 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 @@ -652,12 +649,12 @@ Motif 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 @@ -667,24 +664,27 @@ Conservation tracks 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 :align: center + + 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. Zoom Factor @@ -708,11 +708,13 @@ Dynamic Threshold :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. @@ -732,6 +734,9 @@ information: 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 ~~~~~~~~~~~~~~~~~~~