PeptideAtlas
PeptideAtlas Home
 Seattle Proteome
 Center

  
PeptideAtlas:
  Overview
  Contacts
  Data Contributors
  Publications
  Software
  Database Schema
  Feedback
  FAQ

Atlas Data:
  Data Repository
  Human Plasma
(Farrah, et al.)

  HPPP Data Central
  PeptideAtlas Builds
  Search Database
  

  Contribute Data
  Genome Browser
Setup


Related:
  SRMAtlas
  PASSEL
  Phosphopep
  Unipep
  mspecLINE

Spectral Libs:
  Libraries + Info
  SpectraST Search


Glossary/Terms:
  Atlas nomenclature
  SGD nomenclature
  Protein ID terms

  
  LOGIN

Set Up Genome Browsers

Visualize PeptideAtlas tracks in Ensembl Human Genome Browser


The Human PeptideAtlases have been mapped to the Human genome through Ensembl databases. Ensembl is a DNA sequence assembly project of the EMBL-EBI and the Sanger Center that delivers annotation, predicted genes, predicted proteins and software for research. Ensembl provides a DAS server to browse genome sequence data from many sources.

One can view the most current ISB Human PeptideAtlas tracks in the Ensembl Genome Browser by following the instructions below. Once the ISB tracks have been loaded, our URL's to visualize a peptide will show the peptide in the Ensembl genome browser.

  • Click here to conjure an Ensembl genome view such as the one seen below.


  • In the section titled "Detailed View",

    ⇒select "DAS sources" on the yellow bar,
    ⇒select "Manage Sources" from the list,



  • A window will appear.
    ⇒select "Add Data Source" on the yellow bar, navigation bar.


  • A DAS Wizard for Data Location below will appear.

    ⇒press the "Enter server" button.



  • The window will update to the image below.

    ⇒enter into the DAS Server URL: http"//db.systemsbiology.net:8080/das
    ⇒press the "DSN list" button (do not select "Next").



  • The window will update to the image below.

    ⇒scroll down and check the PeptideAtlas build box for the latest build (e.g. Human_2006_06_Ens39_P09)
    ⇒press the Next button.



  • The window will update to the image below.

    ⇒check Ensembl Chromosome checkbox.
    ⇒press the Next button



  • The window will update to the Display Configuration below.

    ⇒select "Unlimited" rows to display, and press the Finish button.



  • The window will update to the image below.

    ⇒press the Close Window button



  • The original Ensembl Window will then refresh itself to show the track you loaded (see image below).




  • To add other tracks, repeat steps 2 - 9 above.



  • Now links from our Browse Database page coordinates, will display the peptide in the Ensembl genome browser.


© 2004-2014, Institute for Systems Biology. All Rights Reserved
Project funding: