The UCSC Proteome Browser

The University of California Santa Cruz (UCSC) Proteome Browser provides a wealth of protein information presented in graphical images and with links to other protein-related Internet sites. The Proteome Browser is tightly integrated with the UCSC Genome Browser. For the first time, Genome Browser users have both the genome and proteome worlds at their fingertips simultaneously. The Proteome Browser displays tracks of protein and genomic sequences, exon structure, polarity, hydrophobicity, locations of cysteine and glycosylation potential, Superfamily domains and amino acids that deviate from normal abundance. Histograms show genome-wide distribution of protein properties, including isoelectric point, molecular weight, number of exons, InterPro domains and cysteine locations, together with specific property values of the selected protein. The Proteome Browser also provides links to gene annotations in the Genome Browser, the Known Genes details page and the Gene Sorter; domain information from Superfamily, InterPro and Pfam; three-dimensional structures at the Protein Data Bank and ModBase; and pathway data at KEGG, BioCarta/CGAP and BioCyc. As of August 2004, the Proteome Browser is available for human, mouse and rat proteomes. The browser may be accessed from any Known Genes details page of the Genome Browser at http://genome.ucsc.edu. A user's guide is also available on this website.

[1]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[2]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[3]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[4]  C. Chothia,et al.  Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. , 2001, Journal of molecular biology.

[5]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[6]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[7]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[8]  Marc A. Martí-Renom,et al.  MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..

[9]  A. Link.  2-D proteome analysis protocols , 1998 .

[10]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[11]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[12]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[13]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[14]  Narayanan Eswar,et al.  MODBASE, a database of annotated comparative protein structure models , 2002, Nucleic Acids Res..