From 2642cc6fb7c892309145f0b9c035053643371879 Mon Sep 17 00:00:00 2001 From: Brandon King Date: Wed, 1 Nov 2006 17:51:24 +0000 Subject: [PATCH] Mussagl Manual: 1.0 docs part 4 * Updated motif file format * Updated UCSC Genome Broswer section slightly --- doc/manual/mussagl_manual.rst | 36 ++++++++++++++++++----------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index b980016..64dc7c4 100644 --- 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 --------------- -Last updated: Oct 27th, 2006 - -Documentation for Mussagl v1.0 - +Last updated: Oct 31st, 2006 .. Things to add * New features / change log @@ -39,12 +36,13 @@ Documentation for Mussagl v1.0 Status ====== + .. - Major New Features + .. Major New Features .. ------------------ - Change Log + .. Change Log .. ---------- .. INSERT CHANGE LOG HERE @@ -939,12 +937,16 @@ Motif File Format Format: - +:: + + 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 @@ -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 --------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -~~~~~~~~~~~~~~~~~~ +****************** 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 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +************************************************** 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 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +******************************************************* 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. -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +************************************************* 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 -~~~~~~~~~~~~~~~~~~~~~~~~ +************************ 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, -- 2.30.2