vb tutorial-genome browser2010

Karyn Mégy – May 2010 1

VectorBase http://www.vectorbase.org

Genome Browsing at VectorBase

Karyn Mégy��May 2010



Genome Browsing

•  This tutorial will take you through: –  the list of data available (species/type), –  the information available from the main page, –  the entry points to the Genome Browser, –  the Genome Browser (location, gene & transcript tabs), –  adding a track with external data, –  how to search for help!



Species available

•  Invertebrate Vectors of Human Pathogens only ! –  As of mid-2010:

•  mosquitoes (Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus),

•  tick (Ixodes scapularis), •  body louse (Pediculus humanus)

–  Coming next: •  Kissing bug (Rhodnius prolixus) •  Tsetse fly (Glossina morsitans)



Data types available

•  Genomic sequences –  annotated with genes, transcripts, translations etc. –  mapped with proteins and ESTs

•  Proteins from large scope of organisms (taxonomically grouped) and species-specific ESTs

•  External references –  Link between the genes and other databases (e.g.

Swissprot)



Genome Browsing




Example

•  Let’s take the example of Anopheles gambiae, •  chr. 2L : 39,221,590-39,222,203

•  Starting page: http://www.vectorbase.org/Anopheles_gambiae/Info/Index



Main page

•  From the main page: 1- Search for a keyword, 2- Access the genomes, 3- Have a glance at what’s new in the latest release. 4- Access the BLAST, BioMart, FTP and help pages

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Main page

1.  Search for a keyword –  Via popular genome, menu or complete list of species

2. Access the genomes –  in all species or in a given species

3. What’s new –  description of the latest improvements



Main page

4. Access other pages: –  BLAST: compare your sequence to the VectorBase sequences –  BioMart: sophisticated way to mine data and extract complex

queries –  FTP: location to download data files –  Help pages: link to docs, help pages and FAQ

Blast BioMart Help!

FTP



Genome Browsing




Entry points to the Genome Browser

•  From the search box: –  Location, –  Gene or transcript names, –  Function

•  Via the “sample entry points”: –  Location (karyotype,

positions) –  Gene or transcript names,



Genome Browsing

•  Once you’re in the Genome Browser, you see –  Location tab. –  Gene and transcript tabs. ! You need to have selected a gene to see the gene/

transcript tabs.

•  You can navigate by using the left hand side menu or by clicking on the image itself



Genome Browsing




•  From here you can access: - various views for this region: - whole chromosome, - chromosome summary, - region overview, - region in details

- comparative data, - genetic variation ��

& marker data (if available)

•  You can also configure the page and visualise your own data.

Location Tab



Location Tab,��the left hand side menu

Whole genome Chromosome summary

Region overview

Region in detail



Location Tab

•  3 zooms to view context as well as details

•  Default view: genes •  Visualise more data ��

(see later)

Genes



Location Tab,��detailed view

Location��(move to another position/location)

Scale Chr. band

Scaffold name

Strand (+)

Strand (-) DNA

Genes

Features added by configuring

the page (see later)



Location Tab,��did you know?

•  In this tab you can also: –  Export the image (button right),

–  Zoom in or center on a specific region by ��clicking at a position and dragging ��the red window up to the desired location

–  Click on a gene to get more information, and to access the GENE TAB



Gene Tab,��the left hand side menu

•  From here you can access: - gene data - alternative transcript, expression data

- comparative genomic data, - orthologs, paralogs, gene tree

- genetic variations ��(if any available)

- additional data - gene history (over releases)




Gene Tab,��the left hand side menu – gene information

Splice variant

Supporting evidence

External references

Gene sequence

Jump from one view to the other via the menu or the ‘buttons’



Gene Tab,��the left hand side menu – comparative data

Gene Tree

Orthologues

Alignments with other species ��(C.quinquefasciatus in this case)



Transcript tab

•  … •  From here you can access: - transcript data summary, supporting evidence,

sequence, link to external databases - genetic variations ��

(if any available) - protein data summary, domains, variations

- additional data




Transcript tab��the left hand side menu – transcript information

Transcript data

Sequences, Includes individual exons, ��transcript and protein

References to external DBs:��External identifiers,��probes, ontologies



Transcript tab��the left hand side menu – protein information

Protein domain visualisation

Protein domain list

Variation data, Listed only if a variation affects the protein,��i.e. intronic variations are NOT listed in this section (see gene tab for those)



Genome Browsing




Adding external data

•  On the left hand side menu, for each of the tabs, there is a link to ‘manage your data’ or ‘export’ data:

–  Data can be managed by: •  Adding pre-computed data that are not shown by default, •  Adding your own data (see DAS tutorial),




•  Click on ’configure this page’:

•  A pop-up window appears:

Note: depending on the tab (‘location’ or ‘gene’) you’re in when selecting ‘configure this page’, the pop-up window will be different




•  Select tracks and other options in the window, •  Close the popup window, •  The Genome Browser will be updated automatically.

Note: To change whether a track is drawn OR how it is drawn, click on the icon by the track name to select the way the track will be drawn.



Genome Browsing




Help!

•  Multiple Help! points in the Genome Browser: 1- Help button in each view, 2- the pop-up window has documentation at the end, 3- docs and FAQ are available via the top right links, 4- … and you can always contact us via the bottom right link!

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Questions?

* E-mail [email protected]

* Post your question on the forum��http://www.vectorbase.org/sections/Forum/index.php

* Check out the FAQs ��http://www.vectorbase.org/Help/Help:Contents

* Ensembl Genome Browser tutorial��http://www.ensembl.org/Help/Movie?id=188

vb tutorial-genome browser2010

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