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METHODS: Predicting Gene Function From Patterns of Annotation
- Oliver D. King,
- Rebecca E. Foulger,
- Selina S. Dwight,
- James V. White,
- and Frederick P. Roth
Genome Res. May 1, 2003 13: 896-904; Published in Advance April 14, 2003, doi:10.1101/gr.440803
...) Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res. 12 : 203 – 214 . ↵ Schug J. , Diskin S. , Mazzarelli J. , Brunk B.P. , Stoeckert C.J. , Jr. ( 2002 ) Predicting gene ontology functions from ProDom and CDD protein domains. Genome Res. 12 : 648...
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METHODS: The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro
- Evelyn Camon,
- Michele Magrane,
- Daniel Barrell,
- David Binns,
- Wolfgang Fleischmann,
- Paul Kersey,
- Nicola Mulder,
- Tom Oinn,
- John Maslen,
- Anthony Cox,
- and Rolf Apweiler
Genome Res. April 1, 2003 13: 662-672; Published in Advance March 12, 2003, doi:10.1101/gr.461403
....K. , Gubler U. ( 1992 ) Cloning and expression of murine IL-12. J. Immunol. 148 : 3433 – 3440 . ↵ Schug J. , Diskin S. , Mazzarelli J. , Brunk B.P. , Stoeckert C.J. , Jr. ( 2002 ) Predicting gene ontology functions from ProDom and CDD protein domains. Genome Res. 12 : 648 – 655 . ↵ Shields D.C. , Harmon D...
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LETTER: Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database
- Li Li,
- Brian P. Brunk,
- Jessica C. Kissinger,
- Deana Pape,
- Keliang Tang,
- Robert H. Cole,
- John Martin,
- Todd Wylie,
- Mike Dante,
- Steven J. Fogarty,
- Daniel K. Howe,
- Paul Liberator,
- Carmen Diaz,
- Jennifer Anderson,
- Michael White,
- Maria E. Jerome,
- Emily A. Johnson,
- Jay A. Radke,
- Christian J. Stoeckert, Jr.,
- Robert H. Waterston,
- Sandra W. Clifton,
- David S. Roos,
- and L. David Sibley
Genome Res. March 1, 2003 13: 443-454; doi:10.1101/gr.693203
...% of assemblies have similarities to ProDom (available at http://prodes.toulouse.inra.fr/prodom/doc/prodom.html ), whereas ∼10%–12% of the assemblies have significant similarities to Conserved Domain Database entries (CDD; available at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml ) with a conservative...
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RESOURCE: The MicrobesOnline Web site for comparative genomics
- Eric J. Alm,
- Katherine H. Huang,
- Morgan N. Price,
- Richard P. Koche,
- Keith Keller,
- Inna L. Dubchak,
- and Adam P. Arkin
Genome Res. July 2005 15: 1015-1022; doi:10.1101/gr.3844805
...for the domain definition. Homologs The Homologs section displays all BLASTp hits to other genes in the MicrobesOnline database as well as hits to the KEGG ( Kanehisa 2002 ) and SWISS-PROT ( Boeckmann et al. 2003 ) databases, and RPS-BLAST hits to the COG families in the CDD database (Marchler-Bauer et al. 2002...
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Methods: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
- Li Li,
- Christian J. Stoeckert, Jr.,
- and David S. Roos
Genome Res. September 2003 13: 2178-2189; doi:10.1101/gr.1224503
....g., functional assignments based on Gene Ontologies; Ashburner et al. 2000 ; The Gene Ontology Consortium 2001 ; Schug et al. 2002 ), and a multiple sequence alignment of the group members generated using CLUSTALW ( Thompson et al. 1994 ). The graphical representation can be customized to selectively show two...
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ARTICLE: Comparative Analysis of Protein Domain Organization
- Yuzhen Ye and
- Adam Godzik
Genome Res. March 2004 14: 343-353; doi:10.1101/gr.1610504
...and associated tools for efficient recognition of domains in new proteins have been developed, including Pfam ( Bateman et al. 2002 ), SMART ( Schultz et al. 1998 ), PRODOM ( Servant et al. 2002 ), CDD ( Marchler-Bauer et al. 2003 ), INTERPRO ( Mulder et al. 2003 ), DALI ( Holm and Sander 1998 ), CATH ( Orengo...

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