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Literature DB >> 12824422

OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms.

Abstract

OntoBlast allows one to find information about potential functions of proteins by presenting a weighted list of ontology entries associated with similar sequences from completely sequenced genomes identified in a BLAST search. It combines, in a single analysis step, the search for sequence similarities in several species with the association of information stored in ontologies. From each identified ontology term a list of genes, which share the functional annotation, can be retrieved. The OntoBlast function is an integral part of the 'Ontologies TO GenomeMatrix' tool which provides an alternative entry point from ontology terms to the Genome-Matrix database. OntoBlast's web interface is accessible on the 'Ontologies TO GenomeMatrix Gate' page at http://functionalgenomics.de/ontogate/.

Mesh：

Substances：
Proteins

Year: 2003 PMID： 12824422 PMCID： PMC168962 DOI： 10.1093/nar/gkg555

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

14 in total

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Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

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Authors: T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

3. Predicting gene ontology functions from ProDom and CDD protein domains.

Authors: Jonathan Schug; Sharon Diskin; Joan Mazzarelli; Brian P Brunk; Christian J Stoeckert
Journal: Genome Res Date: 2002-04 Impact factor: 9.043

4. Large-scale protein annotation through gene ontology.

Authors: Hanqing Xie; Alon Wasserman; Zurit Levine; Amit Novik; Vladimir Grebinskiy; Avi Shoshan; Liat Mintz
Journal: Genome Res Date: 2002-05 Impact factor: 9.043

5. Association of genes to genetically inherited diseases using data mining.

Authors: Carolina Perez-Iratxeta; Peer Bork; Miguel A Andrade
Journal: Nat Genet Date: 2002-05-13 Impact factor: 38.330

6. Ensembl 2002: accommodating comparative genomics.

Authors: M Clamp; D Andrews; D Barker; P Bevan; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; T Hubbard; A Kasprzyk; D Keefe; H Lehvaslaiho; V Iyer; C Melsopp; E Mongin; R Pettett; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; E Birney
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

7. A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.

Authors: R G Steen; A E Kwitek-Black; C Glenn; J Gullings-Handley; W Van Etten; O S Atkinson; D Appel; S Twigger; M Muir; T Mull; M Granados; M Kissebah; K Russo; R Crane; M Popp; M Peden; T Matise; D M Brown; J Lu; S Kingsmore; P J Tonellato; S Rozen; D Slonim; P Young; H J Jacob
Journal: Genome Res Date: 1999-06 Impact factor: 9.043

8. PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.

Authors: Amit Bahl; Brian Brunk; Jonathan Crabtree; Martin J Fraunholz; Bindu Gajria; Gregory R Grant; Hagai Ginsburg; Dinesh Gupta; Jessica C Kissinger; Philip Labo; Li Li; Matthew D Mailman; Arthur J Milgram; David S Pearson; David S Roos; Jonathan Schug; Christian J Stoeckert; Patricia Whetzel
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

9. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.

Authors: Shuai Weng; Qing Dong; Rama Balakrishnan; Karen Christie; Maria Costanzo; Kara Dolinski; Selina S Dwight; Stacia Engel; Dianna G Fisk; Eurie Hong; Laurie Issel-Tarver; Anand Sethuraman; Chandra Theesfeld; Rey Andrada; Gail Binkley; Christopher Lane; Mark Schroeder; David Botstein; J Michael Cherry
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

10. The FlyBase database of the Drosophila genome projects and community literature.

Authors:
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

38 in total

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Journal: J Struct Funct Genomics Date: 2012-01-22

2. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation.

Authors: Michal Brylinski; Jeffrey Skolnick
Journal: Proc Natl Acad Sci U S A Date: 2007-12-28 Impact factor: 11.205

3. ESG: extended similarity group method for automated protein function prediction.

Authors: Meghana Chitale; Troy Hawkins; Changsoon Park; Daisuke Kihara
Journal: Bioinformatics Date: 2009-05-12 Impact factor: 6.937

Review 4. FINDSITE: a combined evolution/structure-based approach to protein function prediction.

Authors: Jeffrey Skolnick; Michal Brylinski
Journal: Brief Bioinform Date: 2009-03-26 Impact factor: 11.622

5. Proteome-wide remodeling of protein location and function by stress.

Authors: KiYoung Lee; Min-Kyung Sung; Jihyun Kim; Kyung Kim; Junghyun Byun; Hyojung Paik; Bongkeun Kim; Won-Ki Huh; Trey Ideker
Journal: Proc Natl Acad Sci U S A Date: 2014-07-15 Impact factor: 11.205

6. PoGO: Prediction of Gene Ontology terms for fungal proteins.

Authors: Jaehee Jung; Gangman Yi; Serenella A Sukno; Michael R Thon
Journal: BMC Bioinformatics Date: 2010-04-29 Impact factor: 3.169

7. Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks.

Authors: Renzhi Cao; Jianlin Cheng
Journal: Methods Date: 2015-09-11 Impact factor: 3.608