From 337863e85ac1c5604ed7902ff5bceef76a4bbc29 Mon Sep 17 00:00:00 2001 From: Brandon King Date: Mon, 12 Jun 2006 23:32:43 +0000 Subject: [PATCH] Manual: UCSC Genome Browser section --- doc/manual/mussagl_manual.rst | 220 +++++++++++++++++++++++++++++++++- 1 file changed, 219 insertions(+), 1 deletion(-) diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index 317f733..1855192 100644 --- a/doc/manual/mussagl_manual.rst +++ b/doc/manual/mussagl_manual.rst @@ -176,7 +176,225 @@ Now we have found the location of SMN1 on human! :alt: Genome Browser - SMN1 (human) :align: center -FIXME: continue here. + +Step 2 - Download CDS/UTR sequence for annotations +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Since we have found **SMN1**, this would be a convient time to extract +the DNA sequence for the CDS and UTRs of the gene to use it as an +annotation_ in Mussa. + +**Click on SMN1** shown **between** the **two orange arrows** shown +below. + +.. image:: images/ucsc_gb_smn1_human_click_smn1.png + :alt: Genome Browser - SMN1 (human) - Orange Arrows + :align: center + +You should find yourself at the SMN1 description page. + +.. image:: images/ucsc_gb_smn1_description_page.png + :alt: Genome Browser - SMN1 (human) - Description page + :align: center + +**Scroll down** until you get to the **Sequence section** and click on +**Genomic (chr5:70,256,524-70,284,592)**. + +.. image:: images/ucsc_gb_smn1_human_sequence.png + :alt: Genome Browser - SMN1 (human) - Sequence + :align: center + +You should now be at the **Genomic sequence near gene** page: + +.. image:: images/ucsc_gb_smn1_human_get_genomic_sequence.png + :alt: Genome Browser - SMN1 (human) - Get genomic sequence + :align: center + +Make the following changes (highlighted in orange in the screenshot +below): + + 1. UNcheck **introns**. + (We only want to annotate CDS and UTRs.) + 2. Select **one fasta record** per **region**. + (Mussa needs each CDS and UTR represented by one fasta record per CDS/UTR). + 3. Select **split UTR and CDS parts of an exon into separate FASTA records**. + (Breaks up **exons** into CDSs and UTRs.) + +.. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png + :alt: Genome Browser - SMN1 (human) - Get genomic sequence setup + :align: center + +Now click the **submit** button. You will then see a fasta file with +many fasta records representing the CDS and UTRS. + +.. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_submit.png + :alt: Genome Browser - SMN1 (human) - CDS/UTR sequence + :align: center + +Now you need to save the fasta records to a **text file**. If you are +using **Firefox** or **Internet Explorer 6+** click on the **File > +Save As** menu option. + +**IMPORTANT:** Make sure you select **Text Files** and **NOT**, I +repeat **NOT Webpage Complete** (see screenshot below.) + +Type in **smn1_human_annot.txt** for the file name. + +.. image:: images/smn1_human_annot.png + :alt: Genome Browser - SMN1 (human) - sequence annotation file + :align: center + +**IMPORTANT:** You should open the file with a text editor and make + sure **no html** was saved... If you find any html markup, delete + the markup and save the file. + +Now we are going to **modify the file** you just saved to **add the +name of the species** to the **annotation file**. All you have to do +is **add a new line** at the **top of the file** with the word **'Human'** as +shown below: + +.. image:: images/smn1_human_annot_plus_human.png + :alt: Genome Browser - SMN1 (human) - sequence annotation file + :align: center + +You can add more annotations to this file if you wish. See the +`annotation file format`_ section for details of the file format. By +including fasta records in the annotation_ file, Mussa searches your +DNA sequence for an exact match of the sequence in the annotation_ +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. + +.. image:: images/ucsc_gb_smn1_human.png + :alt: Genome Browser - SMN1 (human) + :align: center + +There are two options for getting additional sequence around your +gene. The more complex way is to zoom out so that you have the +sequence you want being shown in the genome browser and then follow +the directions for the following method. + +The second option, which we will choose, is to leave the genome +browser zoomed exactly at the location of SMN1 and click on the +**DNA** option on the menu bar (shown with orange arrows in the +screenshot below.) + +.. image:: images/ucsc_gb_smn1_human_dna_option.png + :alt: Genome Browser - SMN1 (human) - DNA Option + :align: center + +Now in the **get dna in window** page, lets add an arbitrary amount of +extra sequence on to each end of the gene, lets say 5000 base pairs. + +.. image:: images/ucsc_gb_smn1_human_get_dna.png + :alt: Genome Browser - SMN1 (human) - Get DNA + :align: center + +Click the **get DNA** button. + +.. image:: images/ucsc_gb_smn1_human_dna.png + :alt: Genome Browser - SMN1 (human) - DNA + :align: center + +Save the DNA sequence to a text file called 'smn1_human_dna.fa' as we +did in step 2 with the annotation file. + +**IMPORTANT:** Make sure the file is saved as a text file and not an +HTML file. Open the file with a text editor and remove any HTML markup +you find. + + +Step 4 - Same/similar/related gene other species. +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +What good is a multiple sequence alignment viewer without multiple +sequences? Lets find a similar gene in a few more species. + +Use the back button on your web browser until you get the **genome +broswer view** of **SMN1** as shown below. + +.. image:: images/ucsc_genome_browser_home.png + :alt: UCSC Genome Broswer + :align: center + +**Click on SMN1** shown **between** the **two orange arrows** shown +below. + +.. image:: images/ucsc_gb_smn1_human_click_smn1.png + :alt: Genome Browser - SMN1 (human) - Orange Arrows + :align: center + +You should find yourself at the SMN1 description page. + +.. image:: images/ucsc_gb_smn1_description_page.png + :alt: Genome Browser - SMN1 (human) - Description page + :align: center + +**Scroll down** until you get to the **Sequence section** and click on +**Protein (262 aa)**. + +.. image:: images/ucsc_gb_smn1_human_sequence.png + :alt: Genome Browser - SMN1 (human) - Sequence + :align: center + +Copy the SMN1 protein seqeunce by highlighting it and selecting **Edit +> Copy** option from the menu. + +.. image:: images/smn1_human_protein.png + :alt: Genome Browser - SMN1 (human) - Protein + :align: center + +Press the back button on the web browser once and then scroll to the +top of the page and click on the **BLAT** option on the menu bar +(shown below with orange arrows). + +.. image:: images/ucsc_gb_smn1_human_blat.png + :alt: Genome Browser - SMN1 (human) - Blat + :align: center + +**Paste** in the **protein sequence** and **change** the **genome** to +**mouse** as shown below and then click **submit**. + +.. image:: images/ucsc_gb_smn1_human_blat_paste.png + :alt: Genome Browser - SMN1 (human) - Blat paste protein + :align: center + +Notice that we have two hits, one of which looks pretty good at 89.9% +match. + +.. image:: images/ucsc_gb_smn1_human_blat_hits.png + :alt: Genome Browser - SMN1 (human) - Blat hits + :align: center + +**Click** on the **brower** link next to the 89.9% match. Notice in +the genome browser (shown below) that there is an annotated gene +called SMN1 for mouse which matches the line called **your sequence +from blat search**. This means we are fairly confidant we found the +right location in the mouse genome. + +.. image:: images/ucsc_gb_smn1_human_blat_to_browser.png + :alt: Genome Browser - SMN1 (human) - Blat to browser + :align: center + +Follow steps 1 through 3 for mouse and then repeat step 4 with the +human protein sequence to find **SMN1** in the following species (if +you find a match): + + 1. Rat + 2. Rabbit + 3. Dog + 4. Armadillo + 5. Elephant + 6. Opposum + 7. x_tropicalis + +Make sure to save the extended DNA sequence and annotation file for +each one. Using Mussagl ============= -- 2.30.2