CGD Help: Proteome Browser

Contents

• Proteome Browser Description
• Proteome Browser Organization
  • "Search" section
  • "Overview" section
  • "Details" section
  • "Tracks" section
  • "Display Settings" section
  • "Add your own tracks" section

Proteome Browser Description

The CGD Proteome Browser displays primary structural information for CGD proteins. It is adapted from the Proteome Browser developed at the Saccharomyces Genome Database, and is a customized version of GBrowse, a genome browser developed by the Generic Model Organism Database (GMOD) project. The information displayed by the CGD Proteome Browser was generated by searching the organism's protein sequences against the InterPro database of protein domains, motifs and other sequence signatures, using the InterProScan program. Features are displayed according to their position in the protein's primary structure. Hovering the mouse cursor over a feature brings up basic information such as feature type and significance score, and clicking on it links-out to a detailed description provided by the relevant InterPro member database.

Proteome Browser Organization

• "Search" section

  
  • Landmark or Region. Find a different protein for display. Search by gene name, systematic name or keyword.
  • Reports & Analysis. Display or download a summary of the page information by clicking "Go". Change default format or display options by clicking "Configure...". Options include:
    • Download Decorated FASTA File. Optionally configure which features (domains, motifs etc.) to highlight in the sequence.
    • Download GFF File. Download page information as General Feature Format (GFF) file for use on your local system.
    • Download Sequence File. A number of formats are available through configuration.
  • Scroll/Zoom. Control the views in the Overview and Details windows. Arrow buttons control the position, and zoom is controlled with the pull-down menu or +/- buttons. The default zoom is the full-length protein.

• "Overview" section

  

  Graduated scale showing full length of protein. Red box indicates the region of the protein shown in Details window, controlled by Scroll/Zoom option in the Search section. Clicking on the scale re-centers the red box/Details window.

• "Details" section

  

  Presents feature information in tracks along the primary structure of the protein. The lower four tracks display features detected by searching the protein sequence using the InterProScan program.

  • ORF. Track representing the full-length protein. Clicking on the track opens the CGD Locus Summary page for the encoding gene.
  • HMM Domains. Matches to domains defined on the basis of hidden Markov models (HMMs) built from protein families at the member databases comprising InterPro:
    • Pfam
    • SuperFamily
    • Gene3D
    • PANTHER
    • TIGRFAMs
    • SMART
    • PIR
  • Profile/Motif Hits. Matches to specific sequence patterns or sequence alignment profiles, defined at several InterPro member databases:
    • ProSite patterns and profiles
    • PRINTS
    • ProDom
  • Signal Peptide. Matches to signal peptide signatures detected with the SignalP search algorithm.
  • Transmembrane Domains. Matches to transmembrane domain signatures detected with the TMHMM search algorithm.

• "Tracks" section

  

  Allows user control over which tracks are displayed n the Details window, as well as their display order.

• "Display Settings" section

  

  Allows user control over the appearance of the Details window, including size, labeling and highlighting.

• "Add your own tracks" section

  

  Allows the addition of user-defined tracks in the Details window, either via an uploaded file or remote URL.

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