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Literature DB >> 16169922

The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.

Abstract

We developed the Yeast Gene Order Browser (YGOB; http://wolfe.gen.tcd.ie/ygob) to facilitate visual comparisons and computational analysis of synteny relationships in yeasts. The data presented in YGOB, currently covering seven species, are based on sets of homologous genes that have been intensively manually curated based on both sequence similarity and genomic context (synteny). We reconciled different laboratories' lists of paralogous Saccharomyces cerevisiae gene pairs formed by genome duplication (ohnologs), and present near-exhaustive lists of the ohnolog pairs retained in S. cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404).

Entities: Species

Mesh：

Year: 2005 PMID： 16169922 PMCID： PMC1240090 DOI： 10.1101/gr.3672305

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

28 in total

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Authors: Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal: Genome Res Date: 2002-10 Impact factor: 9.043

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Journal: Yeast Date: 1998-03-30 Impact factor: 3.239

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Journal: FEBS Lett Date: 2000-12-22 Impact factor: 4.124

7. Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies.

Authors: J Souciet; M Aigle; F Artiguenave; G Blandin; M Bolotin-Fukuhara; E Bon; P Brottier; S Casaregola; J de Montigny; B Dujon; P Durrens; C Gaillardin; A Lépingle; B Llorente; A Malpertuy; C Neuvéglise; O Ozier-Kalogéropoulos; S Potier; W Saurin; F Tekaia; C Toffano-Nioche; M Wésolowski-Louvel; P Wincker; J Weissenbach
Journal: FEBS Lett Date: 2000-12-22 Impact factor: 4.124

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Journal: Curr Opin Microbiol Date: 1999-10 Impact factor: 7.934

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Authors: G Fischer; C Neuvéglise; P Durrens; C Gaillardin; B Dujon
Journal: Genome Res Date: 2001-12 Impact factor: 9.043

10. Gene order evolution and paleopolyploidy in hemiascomycete yeasts.

Authors: Simon Wong; Geraldine Butler; Kenneth H Wolfe
Journal: Proc Natl Acad Sci U S A Date: 2002-07-01 Impact factor: 11.205

358 in total

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3. Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom.

Authors: Edgar M Medina; Gary W Jones; David A Fitzpatrick
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4. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.

Authors: Ryan J Taft; Cas Simons; Satu Nahkuri; Harald Oey; Darren J Korbie; Timothy R Mercer; Jeff Holst; William Ritchie; Justin J-L Wong; John E J Rasko; Daniel S Rokhsar; Bernard M Degnan; John S Mattick
Journal: Nat Struct Mol Biol Date: 2010-07-11 Impact factor: 15.369

Review 5. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

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Journal: OMICS Date: 2006

6. Functional analysis of gene duplications in Saccharomyces cerevisiae.

Authors: Yuanfang Guan; Maitreya J Dunham; Olga G Troyanskaya
Journal: Genetics Date: 2006-12-06 Impact factor: 4.562

7. PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species.

Authors: Derrick E Fouts; Lauren Brinkac; Erin Beck; Jason Inman; Granger Sutton
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