SESSION 1

SUMMARY

Popular genome browsers are nowadays fundamental in a research lab to access the sequence and the annotations for hundreds of species. Here we will use one of the most popular genome browsers: UCSC. We will focus on the protocol to navigate through the basic information that can be used to annotate genes and regulatory regions in the human genome. Other genomes will be used here to explore comparative genomics capabilities provided by these bioinformatics tools. The most powerful feature of UCSC is how easy is for non-expert users to upload their own data to integrate it with current annotations. Thus, users can save multiple configurations of custom tracks into sessions that are protected under password which can be distributed among collaborators. We will see in this exercise how to create a UCSC account for our sessions, uploading our own custom tracks of annotations in Bed and BedGraph formats.

TABLE OF CONTENTS:

1. Create your session

2. Discovering the interface

3. Playing with tracks

4. Adding custom tracks

5. Bibliography

Step 1. Create a session

[ETC: 5 mins]

Open the UCSC Genome Browser:

[http://genome.ucsc.edu/]

• • Search the Help link (Browser documentation)

  • Read the Getting started using Sessions text

  • Open the Sessions Tool and Create an account

  • Once you receive the confirmation e-mail, activate the link

  • Now, login into your session

Step 2. Discovering the interface

[ETC: 15 mins]

Click the Genomes link in the menu on top:

1. 1. • Select to work with Human

      • Explore the Human assembly box

      • Set the Human assembly to hg38

      • Read the Search the assembly instructions

• • • Search for the LRRTM1 gene (RefSeq Genes track in the output)

    • Notice general features of this gene: location, exons, strand, etc.

• • • Play with the move/zoom in/zoom out/base buttons

    • Practice to drag the landscape or to zoom into the viewer

    • Change the order between tracks by drag and drop vertically

    • Learn to use the reverse and resize buttons

• • • Drag and drop the mouse to select a region (on top of the ruler)

    • First, highlight the region in orange

    • Second, repeat the selection and perform a zoom in, instead

• • • Use View->DNA to get the DNA sequence of the current window

    • Use View->PDF to get a graphical representation of this region

    • Click over the Genome browser link in the menu on top to return

    • Press configure: increase text size and press submit

Step 3. Playing with tracks

[ETC: 20 mins]

Let us focus on the blocks of data tracks:

1. 1. • Press the hide all button

      • Examine the different blocks of options

• • • Find the NCBI RefSeq Genes supertrack into the Genes and Gene Prediction Tracks block

    • Click over the NCBI RefSeq Genes link to recover more information

    • Set UCSC RefSeq subtrack to pack and press Submit

    • Change to dense or squish visibility modes of NCBI RefSeq Genes

    • Use the refresh button for updating the screen

    • Return to pack visualization mode

• • • Click over one RefSeq exon of LRRTM1 in the viewer to access the RefSeq Gene record

    • Use the Entrez Gene, PUBMED and OMIM links to gain knowledge on this gene

• • • Go down to Links to sequence section in this record

    • Learn how to download the protein and the transcript sequences

    • Press over the Genomic Sequence link to open the sequence retrieval interface

    • Extract the CDS sequence of LRRTM1

    • Extract the promoter sequence (1Kb)

• • • Click over the Genome browser link in the menu on top to return

    • Find the Conservation track in the Comparative Genomics block

    • Change the visualization mode to pack and refresh

    • Explore the new tracks added into the screen

• • • Click over the Conservation link or the grey bar on the left for configuration menu

    • Hide all the subtracks

    • Set phastCons alignment for vertebrates to pack and press submit

    • Zoom out 10x and analyze the conservation landscape of the LRRTM1 gene

    • Click with the mouse right button over the Conservation track in the browser

    • Set the phastCons track to dense

    • Click with the mouse right button again and choose View image

    • Click over the Conservation track (left button) to change to full mode

    • Click again over the same track to access to statistics

• • • Click over the Genome browser link in the menu on top to return

    • Go to My Data -> My Sessions

    • In the Save Settings block, save your session as UB_Master_Session1_hg38

    • Use the link to this session to reopen this session in a separate tab

Step 4. Adding custom tracks

[ETC: 20 mins]

We are going to explore how to expand the collection of UCSC tracks:

1. 1. • Click over the Genome browser link in the menu on top to return home

      • Go back to the RefSeq internal entry for the LRRTM1 gene

      • Download the mRNA sequence

      • In the main page, open the Blat program (Tools)

      • Paste the LRRTM1 transcript and press the I'm feeling lucky button

      • Click over the BLAT track in the genome viewer to see the alignments

• • • Try with the Predicted protein sequence

• • • Repeat both BLAT queries but pressing Submit to explore the list of hits

• • • Change to Mouse in the Blat interface and repeat the query of the human transcript

• • • Open the Help->Browser Documentation link

    • Read the Creating and managing custom annotation tracks text

    • Read the documentation on the BED format

• • • Go back to the browser (hg38)

    • Press the Add custom tracks button

    • Copy and paste this line:

chr2 80301878 80304752

• • • Press Submit

    • Press the go button and examine the result

• • • Press the Manage custom tracks button

    • Click over the User track link

    • Edit the track line to have this:

track name=mygene description=text color=200,100,50

• • • Press the go button and examine the result

    • Explore this web to find more RGB colors

• • • Go to My Data -> Sessions and save the session

• • • Open the Help->Browser Documentation link

    • Read the Creating and managing custom annotation tracks text

    • Read the documentation on the bedGraph format

• • • Click over the Genome browser link in the menu on top to return

    • Press Manage custom tracks first and press Add custom tracks after

    • Introduce the following lines:

track type=bedGraph name=myprofile description=text color=50,100,200

chr2 80301000 80302000 5

chr2 80302000 80303000 10

chr2 80303000 80304000 20

chr2 80304000 80305000 10

chr2 80305000 80306000 5

• • • Press the go and examine the result

• • • Open the properties of the myprofile track (link, mouse right button or grey bar on the left)

    • Set the visibility mode to full, the scaling to vertical (min to 0 and max to 20)

    • Change the Track height to 60

    • Go to My Data -> Sessions and save the session

• • • Click over the Genome browser link in the menu on top to return

    • Read the Creating and managing custom annotation tracks text

    • Read the documentation on the interact format

    • Go back to the browser

    • Press the Manage custom tracks button, press Add custom tracks next

    • Introduce the following lines:

track type=interact name="myinteraction" description="text" interactDirectional=true maxHeightPixels=50:50:50 visibility=full

chr2 80301878 80304752 sample 0 1 tissue #00AA00 chr2 80301878 80301878 LRRTM1 . chr2 80304752 80304752 INTERACTION +

• • • Press the Go to genome browser button and examine the result

• • • Go to My Data -> Sessions and save the session

Bibliography

• E. Blanco. Genomica Computacional (spanish, 248 pages). Editorial UOC (2013). ISBN: 978-84-9029-910-4.

• Practical Bioinformatics. Michael Agostino. Garland Science (2012). ISBN: 978-0815344568.

• Genomes, Browsers and Databases: Data-mining Tools for Integrated Genomic Databases. Peter Schattner. Cambridge University Press (2008). ISBN: 978-0521884433.

• Understanding Bioinformatics. M.J. Zvelebil and J.O. Baum. Garland Publishing Inc ,USA (2007). ISBN-10: 0815340249.

• Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition. A.D. Baxevanis and B. F. Francis Ouellette, chief editors. John Wiley & Sons Inc., New York (2005). ISBN: 0-4 71-47878-4.