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 UCSC Proteome Browser User's Guide
  Table of Contents:

Last updated 12 Feb 2004. Questions and feedback welcome.



  Overview
 

The Proteome Browser provides a wealth of protein information presented in the form of graphical images and links to external internet sites.

SwissProt information: The top line of the page shows the SwissProt accession number, entry name, and protein name for the current selection. Click on the accession number to open the record for this protein in the SwissProt database.

Proteome browser tracks: The tracks image displays a set of aligned tracks showing information about the protein's amino acid sequence and anomalies, the corresponding DNA sequence and exon make-up, and protein traits such as hydrophobicity, glycosylation potential, polarity, cysteine content, and SuperFamily domain composition. To display a description of a track from the Protein Browser web page, click on the track's label. For more information about the individual tracks, see the Protein Tracks section.

The navigation buttons permit scrolling and resizing of the tracks image:

  • Scrolling left or right: To shift the browser tracks image sideways to the left or right by 2%, 47.5%, or 95% of the displayed size, click the corresponding move arrow.
  • Rescaling the image: The Rescale to buttons control the size of the tracks image. At the default "Full" setting, the image is displayed at its full size. The "1/2" and "1/6" buttons shrink the image size by the equivalent amount. The image retains its scrolled settings when it is rescaled. The amino acid sequence of the protein is displayed only in the full-sized image.
  • Displaying the Genomic sequence: To view the codons that correspond to the Amino Acid Sequence track and their reverse complements, click the DNA rescale button. The Genomic Sequence track is hidden by default.

Protein property histograms: The Protein Browser's histogram section provides a graphical comparison of several protein traits relative to those of proteins genome-wide. The pictured traits include amino acid frequencies and anomalies, molecular weight, exon count, cysteine abundance, hydrophobicity, isoelectric point, and predicted domains. To display a brief description of a histogram from the Protein Browser web page, click on the graph's label. For detailed information on the histograms, see the Protein Property Histograms section.

UCSC links: These links display additional information about the gene and mRNA associated with the selected protein.

  • Genome Browser link: Click on the accession number to open up a Genome Browser window displaying this mRNA.
  • Gene Details Page link: Click on the accession number to display the Genome Browser Known Genes details page for the gene associated with this protein.
  • Gene Sorter link: Click on the accession number to open up a Gene Sorter window displaying the gene associated with this mRNA, along with a set of related genes.

Domain information: The browser provides 3 primary sources of detailed domain information about the selected protein.

  • SuperFamily/SCOP track: See the Protein Tracks section for a description of this track. Click on a yellow domain box in the track to display Superfamily information about that domain.
  • EMBL-EBI InterPro website link: Click on the Graphical view of domain structure link to open a page showing protein matches from the UniProt-SwissProt database. Click on an ID number to display the InterPro information page for that domain.
  • Sanger Institute Pfam (Protein families database of alignments and HMMs) website link: Click on the Pfam accession number to display the Pfam database record for the domain.

Comparative 3-D structures:

  • Protein Data Bank (PDB): When available, this section displays one or more 3-D structures of the protein from the PDB. Click on a structure number to display the associated PDB record.
  • ModBase: This section displays front, top, and Side views of the predicted comparative 3-D structure of the protein obtained from UCSF's ModBase. Click on the protein accession number or one of the images to display the ModBase database record for the protein. If no images are displayed, no ModBase structure exists for the protein.

Pathways:

  • BioCarta: Provides information about gene interactions within pathways for human cellular processes, displayed on NCI's Cancer Genome Anatomy Project (CGAP) website.
  • KEGG: Displays the associated pathway record in the Kyoto Encyclopedia of Genes and Genomes (KEGG).

Fasta format: This section shows the Fasta record for the protein containing the complete amino acid sequence.



  Protein Tracks
 

This section contains a brief description of the tracks available in the Protein Browser. To view this information directly from the Proteome Browser, click the label of the track in which you are interested.

Amino Acid Scale:

Amino Acid Sequence:

Genomic Sequence and Complement:

Genome Browser:

Exons: For an in-depth discussion of the information displayed in this track, see the Exon Count section.

Polarity: For an in-depth discussion of the information displayed in this track, see the Polarity and Isoelectric Point section.

Hydrophobicity: For an in-depth discussion of the information displayed in this track, see the Hydrophobicity section.

Cysteines: For an in-depth discussion of the information displayed in this track, see the Cysteine Count section.

Glycosylation: For an in-depth discussion of the information displayed in this track, see the Glycosylation section.

Superfamily/SCOP: For an in-depth discussion of the information displayed in this track, see the Protein Domains section.

Amino Acid Anomalies: For an in-depth discussion of the information displayed in this track, see the Amino Acid Anomalies section.



  Protein Property Histograms
 

This section contains a brief description of the histograms available in the Protein Browser. To view this information directly from the Proteome Browser, click the label of the histogram in which you are interested.

pI: For an in-depth discussion of the information displayed in this track, see the Polarity and Isoelectric Point section.

Molecular Weight: For an in-depth discussion of the information displayed in this track, see the Molecular Weight section.

Number of Exons: For an in-depth discussion of the information displayed in this track, see the Exon Count section.

Amino Acid Frequencies: For an in-depth discussion of the information displayed in this track, see the Amino Acid Anomalies section.

InterPro Domains: For an in-depth discussion of the information displayed in this track, see the Protein Domains section.

Hydrophobicity: For an in-depth discussion of the information displayed in this track, see the Hydrophobicity section.

Number of Cysteines: For an in-depth discussion of the information displayed in this track, see the Cysteine Count section.

Amino Acid Anomalies: For an in-depth discussion of the information displayed in this track, see the Amino Acid Anomalies section.



  Exon Count
 



  Polarity and Isoelectric Point
 



  Molecular Weight
 



  Hydrophobicity
 



  Cysteine Count
 



  Glycosylation
 



  Protein Domains
 



  Amino Acid Anomalies