-==============
-Mussagl Manual
-==============
+===================
+Mussagl Manual v1.0
+===================
---------------
Brandon W. King
---------------
-Last updated: Oct 27th, 2006
-
-Documentation for Mussagl v1.0
-
+Last updated: Oct 31st, 2006
.. Things to add
* New features / change log
Status
======
+
..
- Major New Features
+ .. Major New Features
.. ------------------
- Change Log
+ .. Change Log
.. ----------
.. INSERT CHANGE LOG HERE
Format:
- <motif> <red> <green> <blue>
+::
+
+ <motif> <optional name> <red> <green> <blue> <optional alpha>
Example:
- GGCC 0.0 1 1
+::
+ AGTGAG "My First Motif" 0.333333 0.588235 1 1
+ ATGAT "2nd Motif" 1 0 0 1
IUPAC Nucleotide Code
you prefer to skip this section of the manual.
UCSC Genome Browser Method
---------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~
There are many methods of retrieving DNA sequence, but for this
example we will retrieve SMN1 through the UCSC genome browser located
: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:
Step 2 - Download CDS/UTR sequence for annotations
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+**************************************************
Since we have found **SMN1**, this would be a convenient time to extract
the DNA sequence for the CDS and UTRs of the gene to use it as an
Step 3 - Download gene and upstream/downstream sequence
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*******************************************************
Use the back button in your web browser to get back the **genome
browser view** of **SMN1** as shown below.
Step 4 - Same/similar/related gene other species.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*************************************************
What good is a multiple sequence alignment viewer without multiple
sequences? Let'S find a similar gene in a few more species.
Step 5 - Create Analysis
-~~~~~~~~~~~~~~~~~~~~~~~~
+************************
At this point you should have the annotations and fasta files for each
species. If you skipped the first four steps or are having trouble,