From 35a6a66748e82af6eb32149e297a20146edecf3f Mon Sep 17 00:00:00 2001 From: Brandon King Date: Wed, 7 Jun 2006 23:59:45 +0000 Subject: [PATCH] Manual: Progress towards retrieval data for mussa section --- doc/manual/mussagl_manual.rst | 82 +++++++++++++++++++++++++++++++++-- 1 file changed, 79 insertions(+), 3 deletions(-) diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index 938eb07..317f733 100644 --- 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 +`_. + +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 -- 2.30.2