Bioverse: functional, structural and contextual annotation of proteins and proteomes

Functional annotation is routinely performed for large-scale genomics projects and databases. Researchers working on more specific problems, for instance on an individual pathway or complex, also need to be able to quickly, completely and accurately annotate sequences. The Bioverse sequence annotation server (http://bioverse.compbio.washington.edu) provides a web-based interface to allow users to submit protein sequences to the Bioverse framework. Sequences are functionally and structurally annotated and potential contextual annotations are provided. Researchers can also submit candidate genomes for annotation of all proteins encoded by the genome (proteome).

[1]  Susumu Goto,et al.  The KEGG databases at GenomeNet , 2002, Nucleic Acids Res..

[2]  Terri K. Attwood,et al.  PRINTS prepares for the new millennium , 1999, Nucleic Acids Res..

[3]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[4]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

[5]  Amos Bairoch,et al.  The PROSITE database, its status in 2002 , 2002, Nucleic Acids Res..

[6]  Shmuel Pietrokovski,et al.  Increased coverage of protein families with the Blocks Database servers , 2000, Nucleic Acids Res..

[7]  Peer Bork,et al.  Recent improvements to the SMART domain-based sequence annotation resource , 2002, Nucleic Acids Res..

[8]  Alex Bateman,et al.  InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites , 2002, Briefings Bioinform..

[9]  Amos Bairoch,et al.  The PROSITE database, its status in 1999 , 1999, Nucleic Acids Res..

[10]  Masami Ikeda,et al.  Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topology , 2001, Silico Biol..

[11]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[12]  M. Levitt,et al.  A comprehensive analysis of 40 blind protein structure predictions , 2002, BMC Structural Biology.

[13]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[14]  Fan Yang,et al.  TIGRFAMs: a protein family resource for the functional identification of proteins , 2001, Nucleic Acids Res..

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

[16]  Jérôme Gouzy,et al.  The ProDom database of protein domain families , 1998, Nucleic Acids Res..