Manual: Progress towards retrieval data for mussa section

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 938eb0712b7e525a6b633c958dab524e63fb6818..317f733e870be4e3d5a0450144fad498f93931f5 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -7,7 +7,7 @@ Brandon W. King
 
 Last updated: May 23th, 2006
 
-Updated to Mussagl build: 141 (Update to 200 in progress)
+Updated to Mussagl build: 200 (Update to 230 in progress)
 
 
 .. contents::
@@ -101,6 +101,83 @@ Instructions for building from source can be found `build page
 __ wiki_
 
 
+Obtaining Input Data
+====================
+
+If you already have your data, you can skip ahead to the the `Using
+Mussagl`_ section.
+
+Lets say you have a gene of interest called 'SMN1' and you want to
+know how the sequence surrounding the gene in multiple species is
+conserved. Guess what, that's what we are going to do, retrieve the
+DNA sequence for SMN1 and prepare it for using in Mussa.
+
+For more information about SMN1 visit `NCBI's OMIM
+<http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=609682>`_.
+
+UCSC Genome Browser Method
+--------------------------
+
+There are many methods of retrieving DNA sequence, but for this
+example we will retrieve SMN1 through the UCSC genome broswer located
+at http://genome.ucsc.edu/.
+
+.. image:: images/ucsc_genome_browser_home.png
+   :alt: UCSC Genome Broswer
+   :align: center
+
+Step 1 - Find SMN1
+~~~~~~~~~~~~~~~~~~
+
+The first step in finding SMN1 is to use the **Gene Sorter** menu
+option which I have highlighted in orange below:
+
+.. image:: images/ucsc_menu_bar_gene_sorter.png
+   :alt: Gene Sorter Menu Option
+   :align: center
+
+Gene Sorter page:
+
+.. image:: images/ucsc_gene_sorter.png
+   :alt: Gene Sorter
+   :align: center
+
+We will start by looking for SMN1 in the **Human Genome** and **sorting by name similarity**.
+
+.. image:: images/ucsc_gs_sort_name_sim.png
+   :alt: Gene Sorter - Name Similarity
+   :align: center
+
+After you have selected **Human Genome** and **sorting by name similarity**, type *SMN1* into the search box.
+
+.. image:: images/ucsc_gs_smn1.png
+   :alt: Gene
+   :align: center
+
+Press **Go!** and you should see the following page:
+
+.. image:: images/ucsc_gs_found.png
+   :alt: Found SMN1
+   :align: center
+
+Click on **SMN1** and you will be taking the gene expression atlas
+page.
+
+.. image:: images/ucsc_gs_genome_position.png
+   :alt: Gene expression atlas
+   :align: center
+
+Click on **chr5 70,270,558** found in the **SMN1 row**, **Genome
+position column**.
+
+Now we have found the location of SMN1 on human!
+
+.. image:: images/ucsc_gb_smn1_human.png
+   :alt: Genome Browser - SMN1 (human)
+   :align: center
+
+FIXME: continue here.
+
 Using Mussagl
 =============
 
@@ -720,5 +797,4 @@ N   G or A or T or C   aNy
 .. _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
-
+.. _wpDnaMotif: http://en.wikipedia.org/wiki/DNA_motif
\ No newline at end of file