The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.
By Kevin P. Byrne, Kenneth H. Wolfe. Genome Research, 2005
753 citations recorded by the source corpus.
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).
Subfields: Food Science, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/3eb5756758ea22447b10db9b9a730c8f049f4e52
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In Molecular Biology
- Peer Bork
- Christophe Dessimoz
- C. von Mering
- Tobias Doerks
- Adrian M. Altenhoff
- Natasha M. Glover
- Kristoffer Forslund
- Gaston H. Gonnet
Citations in the corpus
- The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements (2014, methodology): “Synteny visualization tools have been successfully developed in several comparative genomics databases such as Yeast Gene Order Browser (39), Genomicus (40) or GnpIS (41).”
- A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation (2014, background): “Among these three validation factors, gene order can identify more accurately the false assignments, illustrating again the need to combine orthology predictions with synteny information where available [27], [38–40].”
- OMA 2011: orthology inference among 1000 complete genomes (2010, background): “The interest for orthology has given rise to the development of several specialized databases, such as COG/KOG (3), InParanoid (4), OrthoMCL (5), YGOB (6), Roundup (7), Homologene (8), Ensembl Compara (9), HOGENOM (10), EggNog (11), MBGD (12), OrthoDB (13), PhyloDB (14) and PHOG (15).”