From 6e7d4a797d7563859ee80cd443ab3bb11bab9079 Mon Sep 17 00:00:00 2001 From: Brandon King Date: Thu, 18 May 2006 23:05:18 +0000 Subject: [PATCH] Manual: Main Window section added --- doc/manual/mussagl_manual.rst | 166 ++++++++++++++++++++++++++++++++-- 1 file changed, 156 insertions(+), 10 deletions(-) diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index 1f348e3..ebf16d3 100644 --- a/doc/manual/mussagl_manual.rst +++ b/doc/manual/mussagl_manual.rst @@ -5,9 +5,9 @@ Mussagl Manual By Brandon W. King ------------------ -Last updated: May 15th, 2006 +Last updated: May 18th, 2006 -Updated to Mussagl build: 141 (Update to 193 in progress) +Updated to Mussagl build: 141 (Update to 200 in progress) .. contents:: @@ -219,18 +219,163 @@ Overview ~~~~~~~~ .. Screenshot with numbers showing features. +.. image:: images/window_overview.png + :alt: Mussa Window + :align: center + +Legend: + + 1. `DNA Sequence (Black bars)`_ + + 2. Annotation_ + + 3. Motif_ + + 4. `Conservation tracks`_ + + 5. `Motif Toggle`_ + + 6. `Zoom Factor`_ (Base pairs per pixel) + + 7. `Dynamic Threshold`_ + + 8. `Sequence Information Bar`_ + + 9. `Sequence Scroll Bar`_ + + +DNA Sequence (black bars) +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. image:: images/sequence_bar.png + :alt: Sequence Bar + :align: center + +Each of the black bars represents one of the loaded sequences, in this +case the sequence around the gene 'MCK' in human, mouse, and rabit. + +FIXME: Should I mention the repeats here? + + +Annotation +~~~~~~~~~~ + +.. figure:: images/annotation.png + :alt: Annotation + :align: center + + Annotation shown in green on sequence bar. + + +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 subsequence and you +may also choose any color for display of the annoation; 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. + + +Motif +~~~~~ + +.. figure:: images/motif.png + :alt: Motif + :align: center + + 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. + + +Conservation tracks +~~~~~~~~~~~~~~~~~~~ + +.. figure:: images/conservation_tracks.png + :alt: Conservation Tracks + :align: center + + Conservations tracks shown as red lines between sequence bars. + +The red lines between the sequence bars represent conservation between +the sequences. 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. + + +Motif Toggle +~~~~~~~~~~~~ + +.. image:: images/motif_toggle.png + :alt: Motif Toggle + :align: center + +Toggles motifs on and off. This will not turn on and off annotations. + +Note: As of the current build (#200), this feature hasn't been +implemented. + + +Zoom Factor +~~~~~~~~~~~ + +.. image:: images/zoom_factor.png + :alt: Zoom Factor + :align: center + +The zoom factor represents the number of base pairs represented per +pixel. When you zoom in far enough the sequence will switch from +seeing a black bar, representing the sequence, to the actual sequence +(well, ASCII representation of sequence). + + Dynamic Threshold ~~~~~~~~~~~~~~~~~ -Zoom -~~~~ +.. image:: images/dynamic_threshold.png + :alt: Dynamic Threshold + :align: center -Sequence Info -~~~~~~~~~~~~~ +You can dynamically change the threshold for how strong of match you +consider the conservation to be with one of two options: -Scroll Bar -~~~~~~~~~~ -.. Moving sequence + 1. Number of base pair matchs out of window size. + + 2. Percent base pair conservation. + +See the Threshold_ section for more infromation. + + +Sequence Information Bar +~~~~~~~~~~~~~~~~~~~~~~~~ + +.. image:: images/seq_info_bar.png + :alt: Sequence Information Bar + :align: center + +The sequence infomation bars can be found to the left and right sides +of mussagl. Next to each sequence you will find the following +information: + + 1. Species (If it has been defined) + 2. Total Size of Sequence + 3. Current base pair position + + +Sequence Scroll Bar +~~~~~~~~~~~~~~~~~~~ + +.. image:: images/scroll_bar.png + :alt: Sequence Scroll Bar + :align: center + +The scroll bar allows you to scroll through the sequence which is +useful when you have zoomed in using the `zoom factor`_. Annotations / Motifs @@ -380,7 +525,7 @@ Example: 1751 2000 Glorp Glorptype -.. _motif: +.. _motif_file_format: Motif File Format ~~~~~~~~~~~~~~~~~ @@ -401,4 +546,5 @@ Example: .. _wiki: http://mussa.caltech.edu .. _build: http://woldlab.caltech.edu/cgi-bin/mussa/wiki/MussaglBuild .. _fasta: http://en.wikipedia.org/wiki/FASTA_format +.. _wpDnaMotif: http://en.wikipedia.org/wiki/DNA_motif -- 2.30.2