Mussagl Manual: 1.0 docs part 4

 * Updated motif file format
 * Updated UCSC Genome Broswer section slightly

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index b980016da46a4b646aca913e529b67fde049c9c7..64dc7c4f1050397510040b5d4b6f784531185285 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -1,14 +1,11 @@
-==============
-Mussagl Manual
-==============
+===================
+Mussagl Manual v1.0
+===================

 ---------------
 Brandon W. King
 ---------------
 
 ---------------
 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
 
 .. Things to add
        * New features / change log


@@ -39,12 +36,13 @@ Documentation for Mussagl v1.0
 Status
 ======
 
 Status
 ======
 

+

 ..
 
 ..
 

-  Major New Features
+  .. Major New Features

   .. ------------------
   
   .. ------------------
   

-  Change Log
+  .. Change Log

   .. ----------
   
   .. INSERT CHANGE LOG HERE
   .. ----------
   
   .. INSERT CHANGE LOG HERE


@@ -939,12 +937,16 @@ Motif File Format
 
 Format:
 
 
 Format:
 

-  <motif> <red> <green> <blue>
+::
+
+  <motif> <optional name> <red> <green> <blue> <optional alpha>

   
 Example:
 
   
 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
 
 
 IUPAC Nucleotide Code


@@ -997,7 +999,7 @@ The SMN1 data retrieved in this section can be downloaded from the
 you prefer to skip this section of the manual.
 
 UCSC Genome Browser Method
 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
 
 There are many methods of retrieving DNA sequence, but for this
 example we will retrieve SMN1 through the UCSC genome browser located


@@ -1009,7 +1011,7 @@ at http://genome.ucsc.edu/.
    :align: center
 
 Step 1 - Find SMN1
    :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:
 
 The first step in finding SMN1 is to use the **Gene Sorter** menu
 option which I have highlighted in orange below:


@@ -1060,7 +1062,7 @@ Now we have found the location of SMN1 on human!
 
 
 Step 2 - Download CDS/UTR sequence for annotations
 
 
 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
 
 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


@@ -1146,7 +1148,7 @@ file. If found, it will be marked as an annotation_ within Mussa.
 
 
 Step 3 - Download gene and upstream/downstream sequence
 
 
 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.
 
 Use the back button in your web browser to get back the **genome
 browser view** of **SMN1** as shown below.


@@ -1191,7 +1193,7 @@ you find.
 
 
 Step 4 - Same/similar/related gene other species.
 
 
 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.
 
 What good is a multiple sequence alignment viewer without multiple
 sequences? Let'S find a similar gene in a few more species.


@@ -1279,7 +1281,7 @@ each one.
 
 
 Step 5 - Create Analysis
 
 
 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,
 
 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,